The Return Part 2: Favorite Son
by Titan5
Summary: An AU version of what happens after the Return, featuring a strong connection between John and Atlantis.
1. Chapter 1

**Note: **This is for Susn, who requested this fic right after The Return aired (bless her patience) and actually outlined much of the plot. Susn, I'm sorry it took so long and I hope it lives up to your expectations. Although I have several chapters rough drafted, it isn't finished yet. I'll try to keep updates frequent, but I'm working off my work computer, which is somewhat limiting. I really wanted to get this going before the "real" part 2 aired in the US (I have no idea why).

**Summary/Spoilers: **This is an AU tag or part 2 of The Return, so obviously many spoilers for Part I of The Return. This is our version of what happened when the puddle jumper with our team went through the wormhole to an Asuran controlled Atlantis. There is a large focus on the connection between John and Atlantis, because we love that and always yearn for more.

**Disclaimer: **I do not own Stargate Atlantis or have any rights to the show or the characters.

The Return Part 2: Favorite Son - Chapter 1

As soon as the jumper burst through the gate into Atlantis, they were under fire, bursts of light flashing as the shots hit the shield.

"I need the door open, Rodney, _now_!" yelled John.

"Just move, I'll have it open when we get there," Rodney yelled back, his fingers working furiously on the keys of the computer.

John responded by moving the jumper up toward the jumper bay, the doors pulling open just as they arrived at the ceiling of the gateroom. The shots diminished as they rose through the jumper bay and toward the now opening roof. A minute later, they cleared the city and took off across the sky. Drones immediately came after them, forcing John to swing the spacecraft first one way and then the other as he took evasive maneuvers.

"I think they're getting closer. Are you sure about this plan of yours?" Rodney hung onto the armrests of the chair, his eyes wide as the ship turned almost on its side.

"Not now, Rodney," said John, focusing all his thoughts on evading the drones seeking to destroy them. One passed by close enough to clip the back edge of the jumper, shaking it roughly. "All right, now I'm really pissed," he muttered, taking the jumper down. "Hang on, we're going in," he warned just before the nose of the ship entered the dark waters surrounding Atlantis.

In contrast to Sheppard's warning, the entry was relatively smooth, more so than his passengers had expected. Rodney's grip on the seat tightened, a move not lost on his friends. A firm hand appeared on his shoulder, startling him until he looked back to see Teyla's comforting smile.

"It is all right, Rodney. We will be fine."

Rodney nodded, trying to seem more confident than he felt. "Yeah, I know. We aren't going very deep, right?"

"Not this time," said John. He made his way through the water, hoping Rodney's jamming device was successfully keeping the Asurans from tracking them for at least a few minutes. That was all he would need.

After several minutes, the ship eased out of the water and slowly set down on a dark pier. "You realize we're on the far side of the city and it's quite a walk to free O'Neill and the Ancients, assuming they're still alive," pointed out Rodney as Sheppard powered down the jumper.

"I know."

"You also know that this part of the city was heavily damaged in the storm and is likely to be unstable,."

John nodded and grinned. "And _you_ will notice that because of that damage and distance, that this part of the city hasn't been repaired and powered up, making it unlikely that there are any working sensors to detect us."

Rodney looked out the window at the dark structures rising before them. "Oh, I knew that. I was just making sure we were on the same track."

John grunted and slapped Rodney on the shoulder as he stood up. "Sure, Rodney." He made his way to the back of the jumper where his team was gathering up their equipment. "Everyone knows the plan, right?"

Nods came from everyone, including Rodney, who had joined them in the cargo bay. "We're ready, colonel," he said, trying to sound more confident than he felt.

"Good. Let's get our people and take back our city." John lowered the hatch and led the way out. When everyone was on the pier, he raised the hatch and cloaked the jumper. "Okay, let's remember where we parked," he said, trying not to dwell on the disaster that had occurred the last time he'd used that phrase.

They carefully made their way through the darkened hallways, slowly closing the distance between them and the holding cells. They were hoping if any humans or Ancients had been taken alive, that they would be in the cells previously used by the expedition to house Wraith prisoners. Their movements became more careful as they entered the functioning part of the city, where the corridors were lighter and they were more likely to find unwelcome company.

John ran his hand along the wall, feeling the familiar hum of his city. _I'm back, _ he told her with his thoughts. He was surprised at the swell of emotion that rushed through him and wondered if it was him or Atlantis or maybe both. He could feel her welcome him and the rush made him momentarily dizzy. Pausing, he leaned against the wall, grinning as the emptiness he'd felt these past few weeks filled. At least now he understood.

"Colonel?"

John looked up at Beckett's whisper, reading the concern on his face. "Sorry, I'm okay. Atlantis is just glad to see us."

Rodney snorted softly. "You mean she's glad to see _you._ Her favorite son has come home to her."

John grinned, undisturbed by Rodney's slightly biting tone. "You're just jealous because she likes me best." He rubbed the wall affectionately. "I'm glad to see you too, girl. Now we have to rescue you from the evil Replicators." _Keep us hidden as long as you can,_ he thought.

Rodney rolled his eyes. "Could we get on with this already, you know, before they discover us and make us die some kind of horrible and painful death?"

John grinned and nodded. "Let's go."

Elizabeth and Carson exchanged a glance, both resisting the urge to roll their eyes at the two juvenile acting adults in front of them. A few minutes later, they arrived at the door leading to the cells, surprised to find no guards in the hall.

John turned to his team. "I'll take point and Ronon, you're right behind me. The rest of you wait until we've cleared it." He turned and paused by he door, waiting on Ronon to get in position right behind him. At the big man's nod, he opened the door and dashed in low, moving quickly to his right. Ronon followed his moves, but went left. Both of them scanned the room, squatted low with their guns up and ready. John was peripherally aware of movement behind the bars, but the rest of the room was empty.

"Colonel Sheppard, is that you?"

John stood up and watched as General O'Neill made his way to the front of the cell. He gave a quick nod to Ronon before walking over to stand in front of the prisoners. "Yes, sir, General. We've come to get you out of there and take back our city."

O'Neill grimaced. "I know I'm going out on a limb here, but I'm guessing General Landry didn't exactly approve this mission."

John shrugged his shoulders noncommittally. "Not exactly, sir. He said something along the lines of taking care of my military future, but I didn't hear exactly what he had in mind. Nothing good, I'm sure. I believe his plan was to blow up the city. We . . . had a little problem with that."

"He wanted to what?" asked Helia, moving up to stand beside the general. "This isn't his city to blow up."

"That's kind of what we thought," said Elizabeth as the rest of the team entered the room.

"That, and we don't leave our people behind. Not even generals, sir," quipped John.

O'Neill quirked one side of his mouth as he bobbed his head once. "It's not that I'm not grateful, because I am, but do you have any idea how you're going to pull this thing off? You may not have noticed, but the Asurans aren't exactly a friendly bunch."

John nodded toward Rodney, who had already disassembled the control panel to the cell door and was working on it. "Step one is to get all of you out of there and I brought a genius with me who just happens to be well-versed on Ancient technology."

Rodney raised one hand without looking up and then continued to work. John exchanged a smile with Elizabeth and Carson.

"Nice, Colonel, but I'm in the company of several individuals who just happen to be living, breathing Ancients and they couldn't get us out."

"If you'll excuse my saying sir, they are inside the cell whereas we are outside the cell. That gives us a bit of an advantage."

O'Neill looked slightly taken aback. "Oh, yeah, I should have thought of that. Must be something about having Replicator hands stuck in my head."

John winced in sympathy, the feeling all too familiar and recent. "I know what you mean, sir. Not a pleasant experience at all."

"Only if you enjoy having your brains scrambled and then turned inside out," murmured O'Neill. "Personally, I'm not a fan, but that could just be me."

"Got it," said Rodney as the shield deactivated and the door opened. He stood back away from the door, grinning proudly.

"This seems too easy to me," said John cautiously.

Rodney's face fell. "Easy? What are you calling easy?"

"Where are the guards?" asked Ronon, his tone and expression showing his support of John's statement.

"They did not feel the need for guards. They are arrogant and have underestimated their enemy," announced Helia. "As I am afraid we have been. We foolishly believed we could not be bested and yet we very quickly were. I will not make that mistake again. Do they know of your presence?"

John nodded. "They know we're around, but they don't know we're in the city yet."

Helia frowned. "They must know you are here. Sensors are active in this section."

John shook his head. "Atlantis can hide us for a while, but we need to get moving. She can only help us so long before the Asurans figure it out."

Helia frowned up at John. "I don't understand, how is this possible?"

Rodney grimaced and sighed. "Because she likes the Colonel, a whole lot. This isn't the first time she's hid his life signs to keep him from being found. He's her favorite you know."

"No, that is not possible. The city is not capable of communicating with an individual on that level." Helia's expression and tone of voice was decidedly skeptical.

"Well, say what you will, but she always responds to gene boy over there like no one else. She'll sing for him and barely hums for the rest of us," said Rodney.

"As much as I'd like to hear about your love connection with the city, I think I'd rather hear about this wonderful plan to save our collective hides about now," said O'Neill. "What did you have in mind?"

John nodded, switching back into military mode. "I'll take Rodney and Elizabeth to the chair room to launch an attack on the Asuran ship in orbit. Ronon, Carson, and Teyla can take the rest of you to spread out and handle the ones in Atlantis. We brought all the anti-Replicator weapons we could get our hands on. You and Mr. Woolsey can go with whatever group you want to and," he turned to Helia, "I'm sure you'll want to decide what your people do."

Helia nodded. "Dolon and I will accompany you to the chair room, as he is our expert on chair operations. The rest can help your people with the forces in the city." She turned to a tall, slender man at her side. "Savill, you will coordinate our forces with Ronon."

The blonde man nodded, determination in his expression as he pursed his lips together.

John nodded at the Ancients. "Is this everyone?"

"No, there are others in the cell adjacent to this one," said Savill.

Rodney grabbed his equipment. "I'm on it," he said as he left the room, one of the Ancients hurrying along behind him.

"The thing is, we have to try and hit them all at once. Our weapons will disrupt them, but after some of them have been hit, the others start to figure out the frequency of the energy burst and adjust to it. We need to try and take them all out in as short a period of time as possible." He saw the general nodding, experience clouding his eyes. "And if we start the chair operations too early –"

"They will shut you down," finished Helia.

"Right," said John. "Atlantis can only shield us for so long and not when we activate the chair. It draws too much power."

Helia narrowed her eyes at him, frowning slightly. "I still don't understand about Atlantis shielding you. If we manage to survive this, we need to talk."

John grinned mischievously. "How about if I tell you a few things about your city and you let me and my team stay around? We've grown rather fond of Atlantis."

Helia cracked a small smile. "If you can truly return control of the city to us, then I will consider it. Perhaps you would be valuable allies after all."

"So, Colonel, are you going to stand around all day flirting with the nearest Ancient woman or are we going to take the city back?" Rodney asked from the doorway.

"We're taking our city back," John said confidently. "General, what do you and Mr. Woolsey want to do?"

O'Neill glanced briefly at Woolsey before looking back at Sheppard. "Give me one of the weapons and I'm going with Ronon. I'd like nothing better than to kick a little replicator ass right now. I think I owe them a thing or three. You'd better take Woolsey with you, though. I don't think he's exactly ready for the front lines just yet."

John nodded, noting the disheveled and frightened man in a suit. "Yes, sir. We'll take good care of him." He turned to his team. "Move out, radio silence until we're in place."

John was disappointed, but not surprised when they arrived at the chair room fifteen minutes later to find it guarded.

"What do we do now?" whispered Rodney as they crouched in the hallway.

John closed his eyes a second, focusing on Atlantis. Abruptly opening them again, he motioned down the corridor, back the way they had come. The team very quietly made their way down the hall until they could duck down a dark side corridor.

"What now, John?" asked Elizabeth. "Can we take them?"

"We could take them, but then the Asurans would know for sure we're here and that would give them time to start adjusting to the weapons. We can't take that chance."

"We could wait to take them until Ronon and the others start their attack," suggested Rodney.

"No, then the ship would have too much warning before I could get drones off. There's another chair that can be brought online and activated. Atlantis can help us override this one so that we can attack the ship at the same time as we attack the Asurans in the city."

Helia frowned and stepped forward. "There is another chair, but it is in the damaged part of the city. We haven't even restored power to that section yet because it's so unstable. How did you know it was there and how do you know it can be used to override this one?"

John grinned. "Atlantis. We told you, she likes me. Come on, we have a stop to make first and it will take several minutes to get there, even if we hurry."

Rodney smirked at Helia as he hurried past, taking in her confused expression. "When it comes to Atlantis, you really do want to be on his side." He rushed down the corridor, followed by the rest of the team and the two Ancients.

oOo

Ronon peered around the corner and quickly pulled his head back. He smiled and nodded to Teyla and then back toward the corner, holding up all five fingers on his left hand. She acknowledged his message with her own slight nod. Teyla turned and slipped down to the end of the hall where General O'Neill waited with three Ancients.

"Ronon has five at this corridor. I will stay and assist him, as there may be others farther down that we cannot see."

O'Neill nodded. "Good. I'll take our new friends the rest of the way to the control room. With us on this end and that . . . Idiot guy on the other, we should be able to get them all."

Teyla raised one eyebrow at him in dismay. "I believe his name was Idaeus."

O'Neill looked slightly flustered as he moved his mouth a few times before getting sound to come out. "Okay, whatever. Why can't they have simple names like Bob or Harry or Tim?"

Teyla's expression sharpened. "Perhaps they find your names to be odd and hard to remember as well."

O'Neill looked at her for a few seconds and then cleared his throat. "I'm guessing we should get to our post now. Good luck."

Teyla smiled and nodded as she watched the general motion to the Ancients with him and hurry down the hall. She found him to be a strange man, but then she still found Sheppard and McKay to be strange as well most of the time. Must be something about Earth men. She steeled herself for the battle soon to come as she made her way back to Ronon.

oOo

John led the way into one of the power control rooms at the outer edge of the inhabited portion of Atlantis. "Rodney, I need you to divert some power." John touched the panel and brought up a map of that section of the city. He looked at it for just a second before pointing. "Here. We need power diverted to this room, enough to activate a chair."

Rodney looked at the schematics and then pushed a few panels. "Maybe . . . I can get you power, but I'm not sure if I can get you enough."

"Do what you can Rodney," said John, watching the scientist work.

Dolon stepped up to the console beside Rodney. "I can help. I'll get the main routing converted and you carry it to the second chair."

Rodney nodded as he continued to press panels. "Yes, yes, that should work."

Less than five minutes later, Rodney pulled his hands back, nodded to Dolon, and turned to face John.

"You have power, but I'm not sure if it will be enough."

John nodded and put his hand on the panel for a few seconds. "We can make it work. Good job, guys. Let's go, we don't have much time."

They hurried out the door and down the corridor, not bothering to be as quiet as before since they were in the damaged outskirts of the city. The halls were dark and debris littered the floor, making the going rough in places. A few minutes after leaving the power control room, John rounded the corner to come face to face with an Asuran. Acting on reflex, he immediately tackled the man, knocking them both to the floor. His head connected with something hard and his vision darkened.

"John, come on and get up, we have to go."

The muddled sounds that had been scrambling around in his head finally clarified into the voice of Elizabeth. His vision finally decided to focus a second later to find her face near his.

"John, are you okay?"

The pilot immediately began sitting up, the urgency of the situation flooding his thoughts. "Yeah, sorry, guess I hit him a little harder than I intended." His head swam for a second before he made out the pile of metal cubes on the floor next to him.

Elizabeth's face was grim. "We had to shoot him."

"Crap! We'd better get moving. They know we're here now." John used the wall and Elizabeth's arm for leverage so he could get to his feet. The hall swayed for a second, but thankfully settled down fairly quickly. John hurried down the hall and around the corner. They were almost there.

"Sheppard, this is O'Neill. We're in position," came the barely audible whispered voice.

Just as quietly, John responded while entering a room and making his way to the chair in the middle. "Give us a second, we had a last minute change of plan." He leaned the chair back as it lit up and concentrated on checking the power levels. The connection to the city slid into place effortlessly and he smiled at her energetic welcome that sent tingles down his spine.

"What's our status?" asked Rodney as he connected his laptop.

"We have enough power now," the colonel responded. Eyes closed, he frowned. "We have some Asurans that aren't covered. I'm sending you the coordinates. See if Ronon has someone to cover them. We have to take them all out at once, especially now that we've hit one."

Rodney touched his radio. "Ronon, we have two Asurans at Level Four, Sector C, near the transporter. Do you have someone?"

"_Teyla can get them."_

"Good. Let us know when she'd in position." Rodney looked back up at Sheppard. "Give her a second to get in position. What about the chair?"

"She's ready. Everything's ready to power up. We've got to hurry though, they're coordinating a search for us. Atlantis wants them out of here." John frowned, anger crossing his face. "They're hurting her."

Rodney opened his mouth to question the statement, but suddenly touched his radio and listened. "They're ready."

"Go!" said John. As he heard Rodney conveying the message over the radio, he began firing drones, focusing his anger on the destruction of the Asuran ship now orbiting the planet. He fired wave after wave until the ship began breaking apart and finally disintegrated into nothing but space debris. Atlantis showed him the victory, sharing the thrill of watching the destruction with her favorite son.

Reports began flowing in through his connection. Atlantis told him of the destruction of Replicators all over the city and he smiled when he realized they were going to succeed.

"The ship is destroyed!" yelled Rodney. "We're doing it. Asurans are falling all over the city." The team from Earth listened as radio reports began coming in.

"We won? We actually won?" asked Woolsey nervously. His face was pale and his hands were shaking, a testament to just how afraid he had been. He looked down at the floor and put one hand on the wall for support. "I just knew we were going to die," he said softly.

"Well done," said Helia, her expression mirroring her surprise at the victory. "I may have miscalculated the value of your presence," she said thoughtfully.

Rodney grinned and nodded. "Well, it's a common mistake. Some of us are actually quite smart. I'd be happy to share some of the many things we have learned and the advancements we've made since coming here."

"Rodney, I think we can worry about that later," said Elizabeth, but she was smiling as well.

"They're gone, all of them," said John hoarsely. The chair deactivated and returned to its original position. "She's safe now."

Helia walked over to stand beside the chair. "Colonel Sheppard, I think you and I have much to talk about. I have never known anyone to connect to the city on that level, although I have heard stories about a very few individuals in the past. There may truly be a place here for you if you are interested."

John grinned broadly. "Oh, I'm interested all right. I've really missed her." He pushed himself out of the chair and took a step toward the door. "I think we should go hook up with . . . " He stopped and put one hand to his head, a sharp pain moving like lightning from the base of his skull to his temples. He could feel his legs giving way, but couldn't seem to call out a warning or ask for help. As he fell forward, voices gave way to garbled noise and darkness, leaving him unaware of the hands that caught him and lowered him to the floor.

TBC


	2. Chapter 2

**Note:** Thank you for the many awesome reviews. I'm glad most of you are enjoying it and I'm glad I could give you a little ATA food. It's a serious addiction.

The Return Part 2: Favorite Son - Chapter 2

Elizabeth stood between General O'Neill and Captain Helia, waiting on the screen before them to come on.

"Okay, the stargate has engaged and you should get visual in just a few seconds," reported Rodney from the console just behind them and to one side. The light flickered across the screen and then General Landry's face came into view.

Elizabeth immediately stiffened in response. "General Landry, we have good news. We have managed to defeat the Replicators with the help of Captain Helia and her forces and take back Atlantis."

Landry did not look happy or convinced. "Well, that is good news if you are indeed, Dr. Weir and not a Replicator copy."

Elizabeth nodded her understanding of his doubts. "I realize this is a lot to take in, but we are in fact the real thing. We were able to coordinate an attack against the Asurans so that there wasn't time for them to adjust to the weapons. They have all been destroyed. The Ancients are making a final sweep of the city now to make sure nothing was missed."

O'Neill took a step closer and looked directly into the camera. "It's me Hank. I'll admit, I didn't even expect a rescue, much less one this spectacular."

Landry scowled at the trio in Atlantis. "You expect me to believe that Colonel Sheppard and his team managed to rescue you and Woolsey and all the Ancients from the Asurans all by themselves."

O'Neill smiled. "Well, actually they managed to free us from the brig and then we all worked together to defeat the Asurans. We had two advantages, the element of surprise and Colonel Sheppard's somewhat bizarre relationship with this city. Were you aware the city will hide him from others when he asks? Even the Ancients haven't figured that one out yet."

"The only thing I know for sure is that Colonel Sheppard disobeyed a direct order, stole government property, and committed a host of other crimes during his little impromptu mission. He drug civilians into his illicit adventure and endangered the entire planet. He was reckless and irresponsible in an act that bordered on treason. If you have indeed taken the city back, then I'll be sending some guards to escort the Colonel back for his court martial. When he was completely ignoring my direct order to abort this fiasco, I promised him I'd see to that it ended his career and I intend to keep my word." General Landry ended his tirade by smacking the desk loudly with his hand.

Elizabeth looked to O'Neill, trying to judge the man's reaction. Even Jack looked surprised by the depth of Landry's anger. Helia quickly interrupted her thoughts.

"General Landry, I assure you that Colonel Sheppard's actions were well thought out and his plan was solid. Need I remind you that if he had not come, your General O'Neill and Mr. Woolsey as well as my crew and I would be awaiting more torture and a painful death from the Asurans. Atlantis would be in their hands and that alone would present a constant danger to Earth."

Landry shook his head. "We have a ship on the way to – "

"Blow up my city," Helia said angrily. "Yes, I know. And they would not have succeeded. The Asurans were prepared for that kind of attack. They were not prepared for the rescue attempt Colonel Sheppard and his team carried out. The Asurans do not think like that so they were not able to anticipate that behavior. Your Colonel Sheppard's _leave no man behind _reasoning does not make sense to them."

Landry's expression didn't waver. "Well, the fact is that we operate by a system of rules and regulations and the Colonel thoughtlessly broke several of those. He will have to return to Earth to face up to his negligence and be punished."

Elizabeth's expression had hardened during the exchange as she wondered how Landry could be so cold and technical in the face of what they had accomplished. "General, Colonel Sheppard will not be going anywhere for at least a few days. He's currently unconscious in the infirmary suffering from injuries obtained while saving this city. I think we at least owe him a chance to be treated and recover a little before you throw him in a cell to punish him for saving the Pegasus Galaxy from being overrun with Replicators."

Landry had not missed the way she worded her request and he wasn't any the happier for it, but he did relinquish some on the time. "Fine. I want to know the minute he is well enough to leave the infirmary and I want to talk to Caldwell the minute the Daedalus arrives to confirm your story."

O'Neill crossed his arms and squared his stance defensively, something he rarely did. "General, you're making a mistake about Sheppard and I _will _fight you on it."

General Landry snorted. "As I would expect, Jack. When I think about it, you two have a lot in common."

"I guess we do, saving the world several times over and such. It does tend to tire one out though. I know Colonel Sheppard will appreciate the chance to rest."

"Just have Colonel Caldwell contact me when he arrives at Atlantis. At least he follows orders."

"And that's pretty much it," muttered O'Neill as the connection shut down and the screen went blank. "So, Dr. Weir, what does Dr. Beckett have to say about Sheppard's condition?"

Elizabeth sighed and rubbed her temple, trying to ignore the pounding headache building behind her eyes. "He isn't sure at this point." She looked at Helia and smiled. "He's working with one of Captain Helia's physicians . . . "

"Emira," said Helia. "She is one of our best."

Elizabeth nodded and smiled. "As Dr. Beckett is one of ours. It sounds like John is in good hands. They didn't know much the last time I talked to them, but that was almost two hours ago and they hadn't had much time to assess John's condition."

"Then I'd like to suggest we go check on the good colonel," said O'Neill. "We might want to forego telling him about Landry wanting to lock him in prison and throw away the key, at least until he's feeling better."

Helia's brow creased as they walked toward the infirmary. "Will General Landry really put Colonel Sheppard in prison? Even after all that he has done?"

O'Neill shrugged his shoulders. "Hank can be a stickler for regulations, more so than me."

"Everyone is more of a stickler for regulations than you . . . except maybe John," said Elizabeth. She laughed at his expression of mock hurt. "Remember, General, I've read your file."

"So you keep reminding me," O'Neill said dryly. "I'll have a talk with Hank, see if I can get him to go easy on Sheppard."

"I'd appreciate it," said Elizabeth. "John doesn't do these things just for the sake of not following orders. He has this passion for saving lives and I think it gives him the ability to see paths open that the rest of us would never even consider. Outcome should count for something."

"I was honest with Colonel Sheppard when I said I wanted to talk to him about staying in Atlantis," said Helia as they turned the last corner and headed down the hall to the infirmary. "If they are going to lock him up on Earth, then I am willing to offer him sanctuary here with us. He risked his life to save us and Atlantis and I will not stand by to see him suffer for that."

Elizabeth nodded toward Helia. "I know he'll appreciate that," she said as they entered the Atlantis infirmary. Elizabeth could see John on one of the beds, asleep or unconscious and surrounded by strange monitors. She immediately headed for his bed, where Carson stood talking with a female Ancient doctor.

"Carson, how's John?"

Carson smiled at her as the two physicians looked her way. "Oh, hello Elizabeth. This is Emira, sort of the CMO of the Ancients. She and her staff have been helping me evaluate and treat the colonel. As you know, we took all my equipment back to Earth. Their monitoring system is wonderful, much more advanced than anything we have."

Elizabeth nodded. "That's good. What can you tell me about his condition?"

Carson sighed and glanced at Emira. She was Carson's height and had blonde hair clipped back away from her face and sea green eyes. "We don't have a complete answer yet as to exactly what happened, but I can tell you a few things. First of all he has a nasty bump on the head from the run in with the Asuran you told me about. We suspect a mild concussion."

"Is that why he's still unconscious?" asked O'Neill.

Emira shook her head. "No, we think that's a result of his interaction with the chair. Apparently he had to redirect some power to the chair to enable it to fire the drones for an extended period, as well as to accurately site the target. That took a tremendous amount of energy from him and it's left him exhausted."

Carson nodded. "We also think that since our physiology is slightly different than that of the Ancients, that the deep connection to Atlantis may leave him drained as well. When we first got him in here, his vitals and EEG readings were all over the board. His electrolytes and brain chemistry are all out of whack as well. We're monitoring him closely and giving him fluids with the appropriate additions to correct his blood chemistry. He's still not back to normal, but things are starting to stabilize."

"How long do you think it'll be before he wakes up?" asked Elizabeth.

"Tomorrow at the earliest. He's showing all the signs of someone suffering from complete exhaustion," said Carson.

Elizabeth frowned and nodded, looking worriedly down at her friend. "Is he going to be okay?" 

"Aye, I . . . we believe that with a few days rest he'll be fine. How did the meeting with General Landry go?"

O'Neill grimaced and pursed his lips. "Not so well. We're going to have to work on him a little between now and the time Sheppard gets released from here."

"Your General Landry wants to put Colonel Sheppard in prison for disobeying orders," said Helia with obvious distaste.

"Well, that's just crazy. It's because of him we were able to save the city," protested Carson.

"Surely he cannot mean it," said Emira.

O'Neill sighed. "Oh, Hank means it all right. I'll just have to use my boyish charm to change his mind." When the others looked at him with complete confusion, he sighed again. "Okay, then Dr. Weir can use her womanly ways. Maybe you and Teyla could team up against him."

Elizabeth snorted and shook her head. "We'd probably have more luck if we just let Teyla loose on him with her sticks. I haven't found many people who can put up much of a fight against that."

oOo

His throat was bone dry. As his thoughts began to come together, he wondered if he'd gone down or gotten lost in the desert. His mind hovered over thoughts of Afghanistan until he realized that wasn't right. His time there had long since passed. Atlantis. They were back in Atlantis. He shifted slightly, recognizing the feel of the infirmary bed, which in turn encouraged him to try and open his eyes.

"That's it Colonel, wake up for us." Carson's voice.

John smiled as he willed his eyelids apart, realizing he could feel the hum of Atlantis. "Doc?"

"You're looking awfully happy for someone waking up in the infirmary," said Carson playfully.

"We got her back, I can feel it."

Carson nodded and patted John on the arm. "Yes, Colonel, we got her back. Your plan worked like a charm."

"That's unusual," John smirked softly. "Is everyone okay?"

"Yes, lad, everyone is okay. A few minor injuries, but you're the only one stuck in here for now."

"Figures. So what's wrong with me?"

"Before we address that, I'd like to introduce you to Emira. She's been helping me with your tests and treatment."

John acknowledged her with a small nod. "Thanks. So, I guess you're keeping Carson here in line."

Emira smiled and looked at the blushing Scot. "Oh, I haven't found that necessary yet. He's behaving himself so far."

Carson cleared his throat and changed the subject. "Tell me how you're feeling, Colonel."

John did a brief inventory and wasn't displeased. "Not bad, a little tired. Bit of a headache. What happened?"

Carson and Emira both nodded as if that was what they had expected. "Well, Colonel, you experienced a mild concussion from that fall you took. Rodney tells us you hit your head on the wall quite hard. We don't think that was the cause of your collapse however."

"Collapse? Must have been after I got out of the chair. That's the last thing I remember."

"It was," said Carson. "After the battle, you apparently stood up and took about two steps before passing out. You were brought here shortly after and your vital signs and chemical balance were very peculiar. It is our belief that whatever you did in the chair to reroute some of the power was the main causative factor behind your blackout."

"Basically, it exhausted you. Your systems were overloaded and trying to do the work anyway," explained Emira.

John didn't look surprised. "It had to be done. It was the only way to get the drones off quickly enough and accurately enough to ensure a victory. How long have I been asleep?"

"Eighteen hours," replied Carson. "And you needed it."

Sounds across the room drew their attention and John looked up to see Helia and Elizabeth walking toward them. Carson took the pause in conversation to shift the head of John's bed up and add an extra pillow behind his back.

"Look who's awake," said Elizabeth. "How do you feel?"

"Not bad, just kind of tired." John looked around to see if anyone else was with them. "Is General O'Neill still here?"

Elizabeth shook her head. "No, he went back to Earth just a little while ago. I think he's supposed to meet with the President and fill him in on what's happened."

John widened his eyes a moment. "General Landry let him go back to Earth? I didn't think he'd believe it was really us, at least not this quickly."

"The Daedalus arrived a bit ago and Caldwell was able to confirm that General O'Neill was in fact General O'Neill."

John sighed, looking disappointed. "Guess that means my days of freedom are seriously limited. So, how quickly does he want my head delivered on a platter?"

"Now John, it's not that bad," said Elizabeth in a voice that didn't sound very convincing.

John grimaced. "Nice try, Elizabeth, but Landry was seriously pissed. I have no illusions about what's about to happen. With my record, they'll lock me up and throw away the key." John studied her expression. "You've talked to him. What did he say?"

Helia spoke when Elizabeth didn't. "General Landry said you were to be escorted back to Earth as soon as you were able. He is sending some men to take you back to Earth when you are released from the infirmary. I would like to intervene, if I may, and request that you be allowed to stay here in Atlantis. I confess to being at a loss to explain your connection to the city and I would like to know more."

"Intervene away, but I doubt it will do any good," said John.

Helia smiled confidently. "Your government wants to maintain contact and establish working relations with us. I will simply make your presence here a stipulation. Your team is welcome to stay as well."

"Well, I'd appreciate that. I think we all would. Atlantis has become our home in the last two and a half years and . . . let's just say we've been missing her since we left."

"I can vouch for that," added Elizabeth, her voice deep with emotion.

"Aye, as can I," added Carson.

Helia nodded and looked down. "I'm afraid I owe you all an apology. We threw you out without so much as giving you a chance to make a case for staying. We were just so . . . "

"Freaked out?" asked John helpfully.

Helia chuckled a little. "Yes, I guess you could say we were . . . freaked out . . . with coming back to Atlantis and discovering we were all that was left. I'm sorry for our lack of compassion."

John waved one hand dismissively. "Don't worry about it. We didn't much like it, but we understood it. This is, after all, your city. We forgot that for a while, but we'll remember that from now on."

"I appreciate that, Colonel. And in some ways, it has apparently become your city too. We can learn much from each other. But it will be at our discretion as to who may stay here."

"Fine by me. I'm just glad to be on the list."

Arguing at the door to the infirmary caught their attention. Two armed marines pushed through the Lantean equivalent of a nurse to walk stiffly over to Sheppard's bed.

"Colonel John Sheppard, we are here to escort you back to Earth," said the larger of the two men.

Carson moved between the marine and his patient. "I hardly think so. Colonel Sheppard has only just regained consciousness and certainly cannot get out of bed and walk. Are you bloody daft? Do you not see the man hooked to monitoring equipment and an IV? I'll . . . we'll not be releasing him to anyone just yet."

The two soldiers looked genuinely confused, obviously not expecting to be turned down in their mission. The tall one looked back at Carson. "When can we take him?"

"Not for a few days. He's . . . he's suffering from radical alteration of his blood chemistry and brain waves. It would be much too dangerous to move him now. He might . . . have a seizure and that could lead to brain damage."

The short soldier frowned, staring at Sheppard. "He doesn't look all that bad to me."

Emira sighed and shook her head. "It's sad really. With this kind of illness, the patient looks deceptively well right up until the convulsions start. Have you ever witnessed a major seizure before, because it can be very unnerving if you don't know what to do."

"Uh, we'll contact General Landry and let him know of Colonel Sheppard's status," said the tall marine, looking worried. "In the mean time, I'm leaving Sgt. Clayton here to stand guard, just so nothing happens to Colonel Sheppard."

Sheppard glared at the men. "Gee, thanks for your concern."

"No problem . . . _sir._" The two men turned and walked toward the door, talking the whole way. When they reached the entrance to the infirmary, the short man took up a post just inside the door while the taller man left.

Helia tapped her radio. "This is Capt. Helia. One of the Earth marines is on his way to contact General Landry. When he has finished, I want to know what was said by each of them."

Elizabeth smiled and nodded. "Thank you." She turned to Carson and smiled as she crossed her arms. "Radical alteration of his blood chemistry? Seizures and brain damage?"

John suddenly furrowed his brow as he looked at Carson. "You were kidding, right? About the seizures."

Carson nodded. "Don't worry, Colonel, we're not expecting any seizures. I was just trying to buy you some time. Although you don't have any business being out of bed just yet and certainly not being marched off to a prison cell."

John's face relaxed. "Thanks, I think."

Helia eyed Emira critically. "Doctor, that was some creative diagnosing."

Emira shrugged her shoulders. "Hey, it could happen."

"Well, thanks for helping me out there," said Beckett. "I hate to deceive anyone, but what they have planned is just wrong. We need give General O'Neill some more time to talk to the right people."

Elizabeth turned to John. "So John, now I'm curious. If you had it to do over again, would you?"

John smiled. "Why wouldn't I? It was the right thing to do, no matter what the consequences. Even if I never see the light of day again, I'll know I did what was right and that it made a difference. No one can ever take that away. And that was pretty cheesy, wasn't it? I don't usually do cheesy. Maybe I am brain damaged."

Elizabeth laughed and patted John's arm. "After what you pulled off, I think we'll forgive you."

John suddenly sobered, looking up at Carson and then Elizabeth. "What about you two? You know when he gets done with me, he'll go after you. He may not be able to throw you in prison since you aren't military, but I'm sure he'll work to get you barred from all things stargate."

"I'd still be here," said Elizabeth firmly. "Carson?"

Carson smiled and nodded. "Definitely. Like you said, Colonel, it was the right thing to do."

TBC


	3. Chapter 3

**NOTE: **Thank you so much for the reviews. I'm sorry I don't have enough internet time to answer them all. Landry is kind of jerk in this one and I'm sorry if that is too out of character. He kind of rubbed me wrong in Part one and I guess I just built on what looked to me like a total disregard of the Atlantis team's knowledge and abilities. He would never have treated SG1 like that. Anyway, sorry if I went overboard.

The Return Part 2: Favorite Son - Chapter 3

John was pretty sure he had memorized every minute detail of the infirmary ceiling. Actually, he'd done that long ago, but he'd spent the last several hours rediscovering everything. It was late and the infirmary was dark, but John couldn't sleep. The hum of Atlantis that had been so welcoming before now seemed to thrum just beneath his skin like an electric current. He'd always felt the connection before, but it usually wasn't so insistent. It reminded him of some long lost relative that was hugging him too tightly and just wouldn't let go. He relished her presence, her touch, but it filled him with a nervous energy that would not allow him to relax.

John longed to get up and walk around, to go to the nearest balcony and spend some time watching the moonlight reflect off the ocean waves. He lifted his head a few inches to see his guard was still standing by the door. He could probably take the guy, but then he'd have to deal with Carson and Elizabeth, so he decided it just wasn't worth it. Sighing, he rolled over for the tenth time that night, trying to untangle the blanket and sheet from around his legs. In the process, he pulled one of the electrode pads off his temple, sending an alarm blaring.

"Well, crap!" He sat up and started to turn around and find a way to turn the machine off, but froze when he heard a gun cock.

"Freeze, colonel!"

John did what he was told, having no desire to be filled full of holes just because he was having trouble sleeping. He raised his hands slowly and turned to face his guard and the gun pointed directly at his chest.

"Sergeant, let's not overreact here. I just pulled one of those lead thingies loose." John was relieved to see Carson and Emira coming out of Carson's office. Or rather Emira's office. He really hated this.

"Put that gun away, it's just the monitor alarm. Colonel Sheppard isn't going anywhere," said Carson sharply as Emira moved past him and turned the alarm off.

"I was trying to turn over and I guess I pulled too hard," explained John. "Sorry."

The soldier finally let his gun drop and nodded, moving carefully back to his position by the door. He never took his eyes off the prisoner he was guarding.

Emira reattached the pad to John's temple and turned the machine back on. "There you go, colonel. All fixed."

John grimaced. "Gee, thanks. I'd rather you just got rid of it."

Carson shook his head. "Not yet, colonel, we're still getting some odd readings in your EEG. I got rid of the other monitors for you, but this one stays a wee bit longer." Carson fixed John's pillows and straightened his covers as he spoke.

"Thanks mom," John said dryly.

Carson smiled and gave a short nod. "You're welcome, son."

Emira watched John's EEG readings for a few minutes before turning back to him. "You can't sleep, can you?"

John sighed and shook his head. "No, not even close. I'd love to get up and stretch my legs, but I'd probably get shot."

"I could give you something to relax you," offered Carson.

"No, no drugs. Besides, I'm pretty sure it wouldn't help. It's . . . " He really hated saying it, always afraid people would think he was nuts or a freak.

"It's Atlantis, isn't it?" asked Emira.

John hesitated a moment, until Carson nodded at him. "Yeah, it's Atlantis. With everything that's happened, she's a bit . . . overenthusiastic right now."

"What does it feel like?" asked the Ancient doctor, leaning a bit closer.

John took a deep breath, hating these kinds of questions. He tried to collect his thoughts into something that sounded reasonably sane. "It's hard to describe, and it's not always exactly the same. Right now I kind of feel like I have one finger in a light socket, but it usually isn't that strong. Unless I'm in the chair and that's . . . that's another world entirely. I can feel her, almost like she's standing next to me. I can tell when new systems are brought on line if they're very big or I'm not doing anything at the time. For example, I think they switched over the power grids about an hour ago. And I'm more in tune with her now than before we got sent back to Earth. It's like . . . she missed me so she's holding on tighter." John rubbed his hand over his face. "Look, I know how crazy that sounds."

Emira shook her head. "No, it's not crazy at all. Carson and I have been studying your EEG. We don't have your previous readings with us right now, but Carson is pretty sure he remembers them enough for us to determine some differences between before you left and now."

John frowned, not entirely sure he wanted to know any more. "Like what kind of differences?"

Carson smiled and patted John's arm, being his usual reassuring self. "Well, lad, you're EEG reading have always been a tad off the rest of us, at least since coming to Atlantis. By talking with Emira tonight and looking at your current readings, I know why. Ancient EEGs have a slightly different pattern than humans and apparently yours are somewhere between the two. Now we aren't talking major changes, so you don't need to worry. But we've noticed some anomalous patterns that appear ever so often that don't match human or Ancient. We noticed one about an hour ago, so I'm assuming those show up when you are having a more direct contact with the city."

"This is really fascinating," said Emira. "I'm hoping Helia works it out so you can stay. Carson and I have already talked about how much we have to learn about how this connection works and why it is so strong in you. Carson said he has extensive DNA studies for you when we are able to get your records from Earth. We want to go back to various test results from your days before Atlantis and compare them to ones done over the years you were here. This is all very exciting."

John stared at the two for several seconds, the feeling of unease growing in him. "So, basically you plan on using me as a lab rat."

The wide smiles on the faces of the two doctors slowly disappeared as they exchanged a look. Carson frowned as he looked down at John. "No, not at all. We just want to run a few tests and, uh, well there is just so much we don't understand and we need to , uh . . . " He sighed and rubbed his forehead for a second. "I guess you're right. We were planning on turning you into a bloody lab rat."

John gave a low, rough chuckle. "It's okay, Carson. I understand that scientific curiosity thing better after spending the last few years working with McKay. And I understand that, for security reasons if nothing else, we really should learn more about the connection and how it works. I just want . . . I want you to remember that your lab rat is human. That sometimes I need a break from it. That sometimes I just need to feel . . . normal for a while." John paused and looked uncomfortable for a moment. "Mostly, I just want to be able to say stop sometimes and have someone listen," he added quietly.

Carson and Emira looked at one another sheepishly and then back to John. "You're right, of course," said Emira. "I guess we just got all caught up in the mystery."

Carson nodded. "Aye, that we did. If we end up staying, I guarantee that we'll ask to do these informative tests, not order and that you will have the option of saying no if you want."

John nodded. "That's all I ask."

Emira smiled. "And in the spirit of listening to our patient, I think we could suspend the EEG monitoring for the night to make it more comfortable for you."

Nodding, Carson glanced around the room before looking back to John. "Aye, and I think we could let you get up for a few minutes to walk around the room a time or two. It's not the balcony, but you could stretch your legs."

John grinned. "Really? What about the IV?"

Carson laughed as he shook his head. "Nice try, colonel, but you'll just have to roll the IV pole around with you. That stays for now."

John was already sitting up and pulling the blankets back as Emira tried to get him to hold still for her to remove the pads on his temples. "First stop is the little pilot's room," John said.

Emira paused and looked at him strangely. "The what?"

Carson nodded toward the bathroom with his head and Emira smiled. "Oh."

John noted the guard tensing and turning toward them, his gun having come partway up. "You better tell the guard what we're doing or we'll all be shot. It'd be just my luck to get killed by our own people for trying to use the bathroom after surviving that crazy mission against the Replicators." He was a little miffed when Carson laughed.

oOo

Carson watched Emira as she studied Sheppard's charts, squinting slightly in concentration. He was pretty sure that her eyes were the brightest green of any he'd ever seen. He smiled, thinking about her easy going manner and light sense of humor. They hadn't been working together long and yet he felt like he'd known her half his life.

"Carson, are you listening to me or daydreaming?"

Carson blinked and focused on what Emira was saying. "What? I'm sorry, I must have let my mind wander," he said sheepishly. Undoubtedly the way to not impress a lady was to totally ignore what she was saying.

Emira just smiled coyly as she looked Carson right in the eyes. "I might be insulted if we hadn't been up most of the night with the Colonel and studying his test results. I know you're tired, though, so I'll forgive you for not paying close attention."

Carson chuckled, relieved that she didn't have her feelings hurt by his inattention. "Right, sorry. I was just . . . " He trailed off as someone entered her office and they both looked toward the door. Carson recognized the woman immediately and stood up, surprise filling his expression.

"Dr. Lam . . . what are you doing here?"

Her expression and tone of voice were flat and completely devoid of emotion. "General Landry has sent me to evaluate Colonel Sheppard's condition to determine if he's fit to be returned to Earth. I'd appreciate it if you would show me to him now."

Carson was speechless, caught completely off guard by the sudden appearance of Landry's daughter. He'd thought they might have a little more time. Realizing what she would find, anger began to fill him. "So, General Landry can't even wait a few days to ruin a man's life for saving a city, almost a hundred lives, and possibly a galaxy. I guess the taste for blood is a strong one."

Lam's face remained emotionless. "I'm just here to do my job, not to make judgment calls on motives. If you'll show me the Colonel, I'll examine him."

"Fine," Carson said angrily, leading the way from the office and making a show of steering around Dr. Lam. His anger increased when he left the office to find four marines waiting outside, presumably to escort the Colonel to his prison cell on Earth. Carson felt his stomach tighten as he tried to think of a way out of the situation.

Sheppard was still dozing when they approached. Around mid-day, he'd said Atlantis was finally beginning to calm back down and the buzzing in his head was laying back enough he could get some rest. Exhausted, he'd slept or dozed most of the afternoon. Almost as if he sensed what was coming, his eyes snapped open at Dr. Lam's approach.

"Colonel Sheppard, good, you're awake. I need to examine you to determine if you are well enough for possible extradition back to Earth."

John looked up at Dr. Lam and then at the four marines standing at the foot of his bed. He sighed, his expression dropping. "Why don't we cut the crap. Landry wants me back promptly for my crucifixion so you're going to find me ready to go. Just yank the IV and let's go. We both know that'll be the end result, anyway."

"I haven't examined you yet, so I don't know what your condition is," said Lam.

John's eyes smoldered with anger. "Yeah, whatever. Well, then do your little dog and pony show of taking a few vital signs so you can declare me ready to travel. Let's just get this over with."

The lights in the infirmary suddenly flickered several times and then went off.

"What's going on?" asked Lam, fear finally putting some emotion into her voice.

"That would be Atlantis," said Emira. "I suspect she's registering her displeasure with your little mission here."

Low level emergency lighting slowly came up, only slightly brightening the dark infirmary. Lam and the four marines were all looking around nervously as if they expected to be attacked.

"You don't seriously expect me to believe a city cares whether we take the Colonel or not. I'm not a complete idiot," said Lam angrily.

John sat up and pulled his IV out, throwing his legs over the side of the bed. Four guns came up and were immediately leveled at him. "Oh, stand down. You want me to go with you don't you. Let's just do this and get it over with. Can I at least put on clothes or do I have to be marched through the city in scrubs?"

Dr. Lam was extremely exasperated by now, having fully lost control of the situation. "I need to examine you first, so please lie back down."

"Colonel, do as she says and lie down. You might as well not make it easy on her," said Carson. Walking over to John, he grabbed band-aide from a nearby cart, wiped the blood from the back of the colonel's hand, and bandaged the wound from the IV.

John pulled his hand back as soon as Carson finished. "No. Look, I just want to leave. If I don't do this now, I won't be able to leave her again. And you're just making it harder on Atlantis. Get my clothes."

Lam was furious. "Fine, we'll go without an exam. And if you fall on your face, it's your fault, not mine. Get his clothes."

One of the nurses brought John's clothes over and handed them to Carson, who then handed them to John. John took them and looked around the room. "I'll see if I can get her to turn the lights back on for you," he said to Carson. A few seconds later the lights flickered and came back on. "I reminded her it wasn't your fault and told her it wouldn't change anything."

Lam glanced nervously around the room, as did the marines. "You . . . you did that?"

John looked at her, his expression hard. "Yeah, she likes me that way. That's something General Landry will never understand. Now, can I dress in private, or did you want a show?"

Lam nodded. "We'll just be waiting out here." She stepped to one side as Carson pulled the privacy curtain.

"I'm sorry, lad. I didn't think they'd come for you so soon," said Carson sadly.

John nodded. "I know. It's okay, Carson, you did what you could and I appreciate that. Tell them to take good care of my girl for me."

Carson nodded. "I will," he said as he moved to the outside of the curtain. He wasn't sure who would be more lost, Sheppard or Atlantis.

oOo

"General Landry, with all due respect, sir, this is very unfair. John . . . Colonel Sheppard is still recovering in the infirmary. The least you could do is wait until he's released. Surely saving this city is worth something." Elizabeth hated feeling like she was begging, but if that was what it took, then she was perfectly willing to do it.

"Look, Dr. Weir, I know since you aren't military, you don't understand the significance of what Colonel Sheppard did. He defied a direct order that was given three times. I can't let insubordination like that go unpunished. I told him I'd make sure his military career was over with if he insisted on going through with his little stunt and he did it anyway. I plan on keeping my word."

Elizabeth gaped at the general on the viewscreen. "_That's_ what this is about, keeping your word to destroy a man because he dared to defy you? Look, General, I realize this seems to you like Colonel Sheppard just ran off half-cocked with no thought to your orders. I can assure you that is far from the truth. It was obvious to all of us with him that he was very concerned about going against your orders, but you have to realize that you were making an uninformed decision. It's not your fault, but you don't know anything about Atlantis or how it works. John knows this place like the back of his hand and he interacts with this city like no one else can. He was the more informed of the two of you and he knew his plan could work. He also knew that there was no way to make you understand that in the limited time available. John did what he did to save a city and a lot of people and he did it knowing that he had a good chance of success."

"General," said Helia, standing beside Elizabeth. "I would once again like to request that Colonel Sheppard and his people be allowed to stay on Atlantis. I realize now that we were a bit hasty in sending everyone back to Earth. We would be very grateful for their help, and perhaps, in return, we could offer our help on certain things. I believe our two people might eventually become allies against a common enemy."

Landry seemed to hesitate a moment, giving Elizabeth cause to hope, when the sounds of people approaching drew the attention of everyone there. She felt like her stomach dropped to her feet at the sight that greeted her. Four marines entered the gate room, surrounding a very pale looking John Sheppard. His hands were bound in front of him, the look of humiliation and defeat on his face enough to make her feel physically sick. He made eye contact with her and nodded, the typical grin nowhere to be found. Elizabeth turned back to screen.

"General, please, don't do this. John is a good man and good soldier. He's given so much of himself the last two years. I just don't understand how you can ignore the sacrifices he's made, the pain he's endured, or the lives that he's saved. How can it be fair to undo all of that because he happened to know more about a conflict situation than you did? Don't make this a personal vendetta."

"Colonel Sheppard will be escorted back to Earth immediately to stand trial. If what you say is true and all of his other accomplishments outweigh this act of defiance, then he'll be acquitted. I also expect you and Dr. Beckett and Dr. McKay to return as well, although since you are civilians, I don't suppose you'll have to stand trial. Consider yourselves lucky."

The lights flickered several times, causing everyone to look around. Elizabeth glanced down at John and he looked up at her and shrugged his shoulders. She couldn't help thinking she'd never seen him look so lost.

"What's going on over there?" asked Landry sharply.

Elizabeth turned back to the screen. "Atlantis doesn't want him to go."

Landry just grunted and shook his head in disbelief. "Putting on your little light show changes nothing. Sheppard will be returned to Earth immediately."

Helia frowned at the general. "Am I to understand that your government does not wish to continue negotiations with my people?"

General Landry shook his head. "No, of course not. The President has expressed a very big interest in continuing our talks. Since you are now willing to have some of our people in Atlantis, I'm sure I could provide equally qualified representatives of our world to come there immediately."

Helia smiled up at the image of the general. "No, you misunderstood my offer. The offer was for Colonel Sheppard and his team. If they are allowed to stay, I will consider letting others come as well at a later date. At this time, the offer is only extended to the Colonel and his people. Now, do you want to work with us or not?"

Elizabeth turned to hide her smile, knowing it wouldn't be seen by Landry as anything good. She looked down at John, his face so full of despair that it almost hurt to look at him. She noticed the marines guarding him looked uncomfortable, as did Dr. Lam standing behind them. Smiling, she winked at him in an effort to pass on her hope and turned back to face Landry. Even though his projected image was a bit fuzzy, she could almost detect the flush of anger in his face.

"General Landry, what will it be?" asked Helia, pressing the man for an answer while she had him pinned down.

Landry finally sighed and nodded. "All right, he can stay for now while I consult with the President. I'll relay your offer to him. Have my people return to the SGC for now and I'll contact you later with our decision. Landry out," he snapped.

Elizabeth suddenly felt so weak and shaky that she wasn't sure she wouldn't collapse on the spot. She looked around at Helia as she gripped the back of the chair in front of her. "Thank you," she managed to whisper.

Helia smiled and nodded. "I meant what I said. I do believe we can learn a lot from each other."

Elizabeth nodded in agreement. "As do I." She turned and took a few steps toward the rail, looking down at the marines waiting below. Savill was with them and apparently conveying General Landry's orders because they were releasing John from the plastic strips binding his wrists together. She thought she heard one of the men apologize to him and then they walked through the still open stargate back to Earth, with Dr. Lam right behind them. As soon as they were gone, the gate was shut down. She headed down the steps, watching John as he stood facing the gate, almost like he was in a trance.

"John?" she called as she rushed to his side. He slowly lowered his gaze to meet hers. "I thought this was it, that I was leaving and never coming back. I don't know how you did it."

Elizabeth grinned as she gripped his hand. "Helia is the one you should be thanking. She told General Landry if you didn't get to stay, then there would be no talks with people from Earth. That got his attention. He knew the President would roast him if he gave up an opportunity to work with Ancients because of his pride."

"I'll never be able to thank you enough," he said to Helia. "Or repay you. But I'll do anything I can to help you, just ask."

Helia nodded as she smiled knowingly. "I'll remember you said that, Colonel. But make no mistake about it, after what you did for us, there was no way you were going through that gate if you didn't want to. If your General Landry had not accepted my terms, we would have simply sent his people home without you. We owe you a debt that I fully intend to honor in every way I can. You are welcome here for as long as you want to stay."

John smiled weakly as he looked around the gateroom, almost like he didn't believe he was still there. "Well, thank you. I think you just evened us up and I'm grateful. I don't really have anything or anyone on Earth I need to return to. This is my home now, and it has been for a while." He looked down at Elizabeth and nodded to her. "This is our home now." He swayed a little as a wave of dizziness hit him.

Elizabeth quickly slid her arm around John's waist, pulling him close in an attempt to get him to lean on her. "Come on, let's get you back to the infirmary before you fall on your face."

"What if I don't want to go back to the infirmary?" asked John.

Elizabeth looked up at him, her expression dead serious. "Where else are you going to go? You don't have a room any more."

John looked at her for a few seconds. "Dang . . . I don't. Guess we'd better go back to the infirmary then."

Elizabeth looked at Helia. "I'll get him back to bed."

Helia smiled at them both. "I need to stay here, but I'll come by later. Welcome back to Atlantis."

John nodded. "Thanks. Okay, let's go." As they headed across the gateroom, John suddenly laughed. "Man, is Beckett gonna be surprised."

Elizabeth gripped John a little tighter as Rodney rushed into the gateroom, almost knocking them down. He was red faced and puffing, his expression one of full blown panic.

"Did I miss him . . . oh . . . you're still here." He looked around wildly before settling his attention back on the two former city leaders. "What's going on? Carson . . . called me and told me . . . they were taking John back to Earth in restraints."

John sighed, but grinned. "Better slow down and catch your breath before you give yourself a heart attack, Rodney. I get to stay."

Rodney's breaths were finally beginning to slow enough to make talking easier. "Really?"

Elizabeth nodded. "Helia told General Landry that if John was forced to go back, they would cut off all ties to Earth. He didn't have much choice after that."

Rodney looked impressed. "Nice move. If Landry pisses off the Ancients, the President will have him for breakfast. I like it." Rodney looked at the way Elizabeth was supporting John. "Maybe you should get him back to the infirmary."

Elizabeth raised one eyebrow. "That's what I was trying to do."

Rodney sidestepped so they could pass and held out his arm dramatically as if ushering them along. "Well by all means, please continue, because I'm not carrying him if he passes out."

"That's good, because I don't want you carrying me."

Rodney looked slightly offended and then fell into step behind them. "Hey, do we all get to stay or just gene boy?"

"McKay, stop calling me that," John snapped.

Rodney grinned silently for several steps. "Hey, if the _gene_ fits . . ."

"Enough," said Elizabeth tiredly. "If you two don't stop, I'm sending you both to bed without supper. I swear, you two would drive Job insane."

Several minutes of silence followed as they walked down the corridor. "Uh, you never answered my question. Do we all get to stay?" asked Rodney in his most penitent tone of voice.

"Everyone but you," quipped John.

"Just arrest me now, because I'm killing both of you at the first opportunity."

TBC

The bad news is that I'll be out of town (yet more science fair) Friday and Saturday, so it will be Saturday night or possibly Sunday before I can post another chapter. Sorry about that. Happy egg hunting.


	4. Chapter 4

**NOTE: **I'm back and sorry for the delay. On a good note, one of our kids got Best in State at the Science Fair! Now I just have to survive a week in Albuquerque next month for the International Fair and I'll be done til next year.

The Return Part 2: Favorite Son - Chapter 4

Helia stepped into the infirmary, her eyes seeking out Colonel Sheppard. He was sitting up in bed with the other people of Earth around him. Smiling, she slipped into Emira's office.

"Emira, I need to talk to you about Colonel Sheppard."

Emira nodded as she stood. "Of course, Captain. Did you want an update on his condition?"

Helia sat down in one of the chairs opposite the desk. "Yes, for starters. Did his little trip to the gateroom yesterday set him back any?"

"No, nothing a little extra rest couldn't overcome. His tests results are coming back almost normal, now, so we're thinking about releasing him tomorrow."

Helia nodded and smiled. "That's good. I guess we'd better find him a room. I need to know what you know about his ability to connect with the city. Is it purely genetic?"

Emira shrugged her shoulders. "I have no idea at this point. We did talk to the Colonel about running some tests and trying to determine why he can do things no one else can, including those of us originally from the city. If his stay is approved by the people of Earth, then we should get his medical records back and Carson tells me there is some extensive information about his DNA in there."

"Good. I'd like you to keep me informed about all of this as you find things out."

Emira frowned just a little as she looked at Helia. "Ma'am, what's going on?"

"I just need to know how he does it and what the extent of the connection is. I need to know if he could override security protocols we have put in place."

"But he just saved the city for us. He wouldn't do anything against us."

Helia leaned forward in her chair. "We don't know these people or their motives. They seem to be genuinely interested in keeping the city safe and letting us be in charge, but I don't want to underestimate them again in case that is not their true concern. The Asurans are not a race to be taken lightly, and yet Colonel Sheppard was able to slip into the city without their knowledge and set up their defeat. I do not want to be caught in a similar situation. I am merely being cautious."

Emira nodded. "Okay, well, I can understand that. I'll let you know anything I find out. Do you want to know what we've found so far? It's not much."

"Yes, I do."

Emira quickly filled Helia in on her and Carson's conclusions concerning Sheppard's EEG and her discussion with the Colonel on what the connection felt like. "I told you there wasn't much," she concluded.

Helia took a slow, deep breath and then blew it out as she thought. "All right, that's a start. Keep me informed. From our end, I'd like to get him to sit in the chair and do some things so that Dolon can analyze the connection."

"He shouldn't connect through the chair for several days at least. Even if we release him tomorrow, it'll be with orders to get plenty of rest and not to do anything strenuous, including work from the chair. Even though his blood tests are normal again, he is still suffering some headaches and dizziness. He needs more time for a full recovery."

Helia stood. "Just tell me when he's ready. I'm not out to hurt him, I just want to understand this better. The more we know, the better ally he can be." She turned and walked out the door, leaving Emira with an uneasy feeling as she followed her into the main infirmary.

"Good morning, Colonel Sheppard," greeted Helia as they approached. "How are you feeling this morning?"

John nodded toward the two Ancients. "Pretty good. Headache's better and I'm not as tired."

"That is good to hear," said the Captain. "I was just telling Emira that we need to find you some quarters soon. Have any special requests?"

"Hmm, something near the others. If you have one close to a balcony, that would be great."

Helia smiled and nodded. "I seem to recall a similar request from Dr. Weir. It seems you are both taken with the balconies of Atlantis."

John looked at Elizabeth to find her looking at him. They locked eyes, both remembering times when they had met on the balcony near the control room to argue, discuss, or comfort one another. "I guess you could say we've logged a lot of quality time out there. We've grown to . . . appreciate it."

"I think you will find that many of us feel the same way," said Emira.

"I believe we have something suitable and near the other rooms. As a matter of fact, it is just down from Dr. Weir's room. I will be happy to take you there as soon as you are released."

John opened his mouth and then closed it, looking surprised. He then looked from Rodney to Elizabeth to Carson. "We don't have any clothes . . . or anything else."

Elizabeth laughed and Rodney rolled his eyes before responding. "Yes, we've noticed since we haven't been lounging around in the infirmary in scrubs. But thanks for pointing out the obvious."

Elizabeth gave Rodney a stern look before returning her gaze to John. "I should be hearing from General Landry today to find out the SGC's final decision on us staying in Atlantis. If it's been approved, the first thing I'll request is that we be allowed to collect our things from Earth. With the city having three ZPMs, we can gate to Earth and gate back the same day."

Carson's face brightened. "Oh, then I could check on my wee baby turtles. I hope they aren't dead."

"I'm sure they're fine Carson, but please don't bring them back here," said Rodney with an eye roll.

"No, no, I'll find a home for them in their own galaxy," assured the doctor.

"I think I'll just stay here, if it's all the same to you guys. If I go back, I'm not sure Landry won't find some reason to keep me there," said John.

Rodney stood and took a step closer to the bed. "How much stuff do you have? Maybe we could get it for you. Although I'm not sure if they'll let us close down your apartment or whatever and turn off all your utilities."

John seemed to sink lower into the bed and chewed on his lower lip a few seconds. "Uh, I don't have an apartment. All my stuff is in my room or my office at the SGC."

All three of the people from Earth looked shocked. "John, we were there for weeks. You never got an apartment or a house or something?" asked Elizabeth.

John shrugged his shoulders. "No. Don't get me wrong, I looked at several places, but they just . . . they didn't seem right. They didn't feel . . . like somewhere I could live. There was something missing, something that made them feel all wrong."

"Atlantis," said Rodney. "You're used to Atlantis. You're always saying how you can feel her. That's what they were missing."

John squirmed under the covers, rolling the edge of the blanket between his thumb and finger. "Maybe. It wasn't the same at the SGC either, but it was a place to stay that was free and handy. Anyway, it won't take long to gather my belongings. I'd appreciate it if one of you could just stick everything in a box or something."

Elizabeth looked sadly from John to Rodney and then back to John. "We'll take care of it if our return is approved. Don't worry. Anything else?"

John rubbed the back of his head. "I guess you can leave my bank account since I won't be needing money here. I never changed it from what I had when we were here before, so it's okay if there's no activity for a while. Who knows, if this all blows over, maybe I'll go back for a vacation or something and need money."

"Dr. Weir," said Helia. "It's getting close to the time to contact your people on Earth. We should get to the control room."

Elizabeth nodded. "Yes, you're right. John, get some rest and I'll stop by this afternoon."

"Okay. Let me know what Landry says." John made a face that registered his distaste. "You know . . . maybe I should be there and . . . apologize to Landry in person."

"You haven't been released yet, Colonel," said Carson.

"It wouldn't take long and I'd come right back," said John. Apologizing to Landry was the last thing on John's list of things he wanted to do, just below getting bitten by another iratus bug, but he knew he owed the man that much. Landry was a general and Sheppard was just a lieutenant colonel. Rank had to mean something, even if it didn't necessarily guarantee that the individual in charge was making the best decision.

"Please, Carson . . . this is important." John knew he could wait, but for the apology to be halfway effective, it needed to be immediate.

Carson sighed and looked at Emira, who smiled at him and nodded. "Alright, Colonel. The Ancients seem to have the equivalent of a wheelchair. If you'll agree to ride in one, you can go make your apology and come right back here."

John smiled and nodded. "Thanks." Emira had already disappeared and returned a minute later with something that did look almost exactly like the wheelchairs from Earth.

Carson insisted on helping John from the bed to the wheelchair, even though the pilot was certain he could do it himself. The doctor covered the Colonel's lap with a blanket and then pushed the chair behind Helia and Elizabeth to the control room. Rodney walked beside them. Ronon and Teyla decided to spar, not really wanting to listen in on the exchange with what they considered the idiots from Earth.

John was self conscious about being wheeled through the hallways like an invalid, even if he didn't know any of the people, er Ancients, they passed. He could feel the stares burning a hole in his back and he was beginning to regret his little request.

When the horrid journey was finally over, Carson parked the wheelchair in front of the screen while Elizabeth stood to his right and Helia to his left. Rodney and Carson stood just behind him and he was grateful for the friends surrounding him. He could feel their strength and determination. John smiled at a sudden rush of what could only be described as support. Atlantis was with him as well.

The screen popped on, surprising him. Generals Landry and O'Neill stood side by side.

"Greeting from Earth," said O'Neill, prompting a partial eye-roll from Landry. "Hey, Sheppard, is that you?" O'Neill squinted and leaned forward just a bit. "Why are you so short?"

"He's in a wheelchair, General. Colonel Sheppard hasn't been released from the infirmary yet, but he wanted to be here for this conference," said Elizabeth.

Landry ignored the reference to Sheppard. "Captain Helia, I have relayed your offer and the . . . conditions, to the President and he . . . has agreed. Colonel Sheppard and his team will be allowed to stay there with our full support. The President wishes me to relay his desire for us to continue relations and his hope that one day we can trust one another and be strong allies."

Helia smiled and nodded. "I think that will be possible. We just need to time to adjust to being home again and to the . . . things that have transpired. I hope you understand. Once Colonel Sheppard and his team have spent some time with us, we anticipate inviting more of your scientific community to join us here. We look forward to getting to know your people better. I'm sorry for the way the offer came about, but you have to understand. Colonel Sheppard and his team gave us our city back. We owe them this much."

"I understand your point of view, Captain," said Landry. "I don't have to like it or agree with it, I just have to honor your request."

"General Landry, sir. I have something I'd like to say if you'd allow it." Sheppard was sitting stiff and straight in the chair, wishing he could stand without Carson shoving him back down.

"Colonel, you know how I feel about this," said Landry.

John felt the heat as his face flushed. "Yes, sir, I know. I just wanted to apologize, sir. I'm not saying I'm sorry we came here or did what we did. But I am sorry I didn't find a way to explain this to you so that you could better see my side of things. I'm sorry if you got the impression I was being disrespectful, because I assure you that my actions were not intended that way. Sir, I think you're a good leader and that you do a great job at the SGC. But Atlantis is my territory and I . . . knew I had the detailed intel on what would and wouldn't work. But I did not take disobeying orders lightly and I never meant it as an act of rebellion or defiance. I know none of that really matters, but I wanted you to know." John forced himself to maintain eye contact during his monologue.

Landry sat quietly for several moments while everyone waited for his response. He finally sighed and rubbed his eyes before dropping his hand. "Sheppard . . . I still think what you did and the way you did it was wrong. The chain of command is here for a reason." He gave a short sideways look at O'Neill before returning his eyes to the screen and continuing. "But Jack had been doing some . . . explaining and I think I at least have a better grasp of what was going through that pig-headed skull of yours. Just be glad Captain Helia came to your rescue and you better not ever try anything like that around me again."

John nodded, not sure if his apology was accepted or not, but at least Landry wasn't spouting death threats or shouting treason at him. "Yes, sir. Thank you, sir. And thank you General O'Neill."

O'Neill just gave a small wave. "Hey, I've been in a few tight spots for similar things over the years. I think I owed someone out there for getting me past all that without a court martial."

"It doesn't hurt that he saved your life," added Rodney.

"There is that," admitted O'Neill.

Landry lifted his chin towards the Ancient. "Helia, I have to ask. If we had taken Sheppard back to Earth, would you have really cut off talks with us?"

Helia smiled. "You would not have been allowed to take Colonel Sheppard. I gave him my word I would offer him sanctuary if he desired it for saving the city and my people. We would have simply overpowered your men and sent them back empty handed and then, yes, we would have closed Earth from the stargate."

"I had a feeling you were serious. Guess we made the right decision."

"Yes, you did."

"General, we have a favor to ask," said Elizabeth. "We would like to return to Earth to collect some things and then return to Atlantis."

Landry and O'Neill looked at one another and O'Neill smiled. "You owe me fifty bucks, Hank. I _knew_ I should have gone for a hundred."

"I misread this one, too. Maybe I'd better reevaluate this whole head of the SGC thing," complained Landry. He shook his head a couple of times before looking back at the people in Atlantis. "That's fine, Dr. Weir. Just let us know when you want to come."

Elizabeth frowned and glanced back at Rodney, Carson, and John, who looked equally confused. She turned back to the screen. "General? What was that about?"

O'Neill looked very smug as he explained. "After the decision was made to let you stay with the government and the military's full support, I bet Hank that you would immediately ask to come back and collect your stuff. Hank bet that you would wait and ask to do that later, after you worked up your nerve. Obviously, I won." He sighed loudly. "Guess they didn't make me general for nothing."

"It really wasn't fair. You worked with Dr. Weir before the Atlantis expedition and I didn't," complained Landry.

O'Neill just shrugged his shoulders. "Okay, Elizabeth, what'll it be? Tomorrow morning work for you?"

Elizabeth had one hand over her mouth trying to hide the unprofessional snicker that was building. What she had dreaded as a confrontation had somehow dissolved into what seemed like a snark session between two generals. That was something you didn't see everyday and she was pretty sure it only happened when O'Neill was one of the generals.

"Tomorrow morning will be fine, Generals. Say, 0800 Atlantis time."

"We'll see you then. And . . . thank you, both of you." Elizabeth bobbed her head in a short nod.

"Earth out," said O'Neill just before the screen went blank.

"Well . . . that went well . . . kind of frighteningly so," said John.

"Aye," said Carson. "I was expecting more fireworks."

"Yeah, me too," said Rodney. "What just happened?"

Elizabeth smiled. "I heavily suspect General O'Neill happened. He understands our predicament better than anyone outside the city and, although he may not admit it, he has a lot more in common with John than he'd care to admit."

John narrowed his eyes and tilted his head. "What does that mean?"

Elizabeth smiled cryptically. "It means he just saved our butts, simple as that."

oOo

John watched Emira finish making notes on his chart and then stare at it expectantly. He wasn't sure if the doctor was having second thoughts about releasing him or just prolonging his agony. "You _are _going to release me, right?" he asked.

A smile crept across Emira's face, even as she tried to stifle it. She finally lowered the datapad and looked up at John. "All right, Colonel. I'll release you under these conditions. First, let us know if the headaches get worse or more frequent, and the dizzy spells as well. Second, you are not on duty, so rest and don't do anything associated with working. That includes sitting in one of those chairs."

John nodded. "I know the drill by now. Did Carson tell you to say all that?"

Emira's eyes twinkled and she grinned. "He did mention it couldn't hurt to remind you. He said that sometimes you . . . forget."

John grinned and shrugged his shoulders. "I'm easily sidetracked. Besides, it's not like I actually have any duties any more and I'm definitely not in charge of anything. What am I going to do, take one too many walks?"

Emira's expression sobered. "How are you handling that, Colonel? It can't be easy to go from second in charge of the whole city to being just a guest."

John rubbed the back of his neck. "Well, it hasn't been a problem so far because I've been stuck in here the whole time. I imagine it will be weird though."

They both turned their attention to the door as Helia walked in and straight over to where John sat on the edge of the bed. "Good morning, Colonel Sheppard. Have you been released yet?"

John looked at Emira hopefully. "Are we done?"

"Yes, Colonel, we're done. Remember your instructions and I expect to see you here for a check up in one week, earlier if you have any problems."

John nodded as he slid off the bed. "You got it, Doc. You don't happen to have my clothes, do you?" He looked down at the white scrubs and decided he really didn't want to parade the halls in them, especially after the wheelchair show.

"They have been cleaned and are in your quarters," said Helia.

John's eyes widened. "I have quarters?"

Helia laughed softly as she nodded. "Yes, you do now. That's why I'm here, to take you to them if you're ready."

"Hey, I'm ready, lead the way." He followed behind her a few steps, the scrubs forgotten, and then paused in the door way. "Thanks, Doc." Without waiting for a reply, he turned and hurried out into the corridor to catch up with Helia.. They arrived at his new room ten minutes later.

John walked in the dark room behind Helia, the lights coming up as they entered. The room was almost exactly like his old room, with the bed in a slightly different place. There was a desk with a lamp and a dresser, but not much else. The bed was freshly made and his neatly folded uniform lay on top. A small table with two chairs sat in one corner.

"This is great, almost like my old quarters," said John, trying to seem grateful. The room felt cold and empty, but he reminded himself that the others would return with his belongings that evening. It wouldn't take much for it to feel like home again, more so than any of the apartments he'd looked at on Earth.

"Your friends should be back in a few hours," said Helia, almost as if she was reading his thoughts.

"Yeah, I know. Everything is just kind of . . . weird."

Helia smiled knowingly. "Like you came home and strangers had moved into your home?"

John sighed and lowered his gaze. "Yeah, exactly like that. I guess you'd know about that feeling, huh."

"Yes, I would, and I know it's a painful one. Give it some time. Maybe we'll both get over that feeling."

John looked up sheepishly. "I hope so. Look, I'm sorry if we . . . intruded where we weren't meant to be. We thought all the Ancients ascended a long time ago. We didn't see the harm."

Helia shook her head. "No, do not be concerned about that. We would have done the same in your position. And it is very possible your coming to the city before we returned was best for all. Now, I know Dr. Beckett wanted you to rest, so if you don't need anything, I'll get back to my duties."

John twisted his face in an expression of distaste. "All I've done is rest."

"Give yourself some time, Colonel. When you have regained some of your strength, we can take a look at the city together. I'd be very interested in hearing about how your people used some of the rooms and technology."

John nodded. "I'd like that, although Rodney's probably the one you should talk to."

"Actually, Dr. McKay has informed me, as well as several of my staff, of a great many things."

John chuckled. "So you've been introduced to the mighty mouth of McKay. Has anyone been able to keep up with him?"

Helia sighed. "I think they've all given up, to be honest."

"He can be . . . annoying and rude, but he really is a genius and he's pulled off the impossible to save us more times than I can count. And if you tell him I said that, I'll deny it with my dying breath."

"It'll be our little secret, I assure you. He doesn't seem to need his ego fed. I'll leave you and let you get that rest. I'll let you know as soon as your people are back." Helia gave one final nod and left the room.

John sat on the edge of the bed, staring at his clothes and deciding if he wanted to bother with getting dressed. He'd been so elated to get out of the infirmary and to be back in Atlantis, and now he was thoroughly depressed. He missed his team, even though he knew Carson, Rodney, and Elizabeth would be back that night. He wasn't completely sure where Teyla and Ronon were.

To make things worse, his discussion with Emira about him having no real job any more was just beginning to sink in. He looked around his bare room and decided the emptiness was making his mood worse. Grabbing his clothes, he headed for the shower.

Fifteen minutes later, he left his quarters and went directly to the balcony down the hall. He'd recognized the area immediately and knew instantly where everything was. Walking out into the light breeze, he felt the warmth of the midday sun on his face. He stood at the rail for while, just breathing in the salt air and looking at the towers of the city and the rolling waves beyond. After a few minutes, he began to relax and fully realize that he was at home. He laughed at his momentary bout of depression, feeling silly and unappreciative.

He got tired after a while and looked around, remembering that they had taken their lawn chairs back to Earth. Walking over to the wall, he sat down so that his legs were stretched out in front of him and his back was next to the structure. There was a slight tingle as he felt Atlantis's touch and he shivered before settling into it.

He was wary of Helia. She had helped them tremendously, but he also knew she was extremely interested in his link to the city. He was pretty sure that had been the deciding factor in offering them protection, more so than their rescue of the Ancients. He didn't much care, as long as they didn't end up being another backstabbing group like the Genii. He knew she didn't trust him as much as she let on, but that didn't bother him. He didn't completely trust her either. John sincerely hoped he was just being paranoid.

oOo

"He's stopped moving. He's on the balcony near his room and he seems to be staying put."

Helia nodded to Savill as she looked over his shoulder at the screen. "Okay, just have someone keep an eye on his movements. Let me know if he goes to any sensitive areas so we can intercept him and find out what he's doing."

Sevill turned to the Captain, uncertainty in his face and voice. "Do you think he is here for reasons other than he said?"

Helia let out a long breath. "I don't know at this point, it's too early to tell. I'd like to believe him and his friends, but it takes time to build trust. We can't just assume they are being honest with us. I will not chance losing Atlantis again. Just keep an eye on Colonel Sheppard and the others until further notice. Where are the the Satedan and the Athosian woman?"

"They are still engaged in training exercises with my men. They have some very unique techniques, some of which I think would benefit our forces. The woman, Teyla, you should see her with her sticks. It's amazing."

Helia nodded and smiled. "I think I may drop by and try to do just that. The Athosians were always a strong and proud people. I'm glad to hear that hasn't changed."

"We could have let them stay on the mainland."

"No, that would not have been prudent. They depend on access to the gate for trade and that made them dependent on us. It is better that they have their own gate and can be independent. They were leaning on the people of Earth far too much."

Savill nodded. "I understand."

"Get someone to keep an eye on the Colonel and then let's go have a look at the training exercises. I'd like to see Colonel Sheppard's teammates in action. Whether they end up being allies or enemies, we need to understand them, know their strengths and weaknesses."

Savill snorted. "Good luck finding any weakness in Ronon. He's flattened everyone we put up against him so far."

"Let's hope they end up being allies, then."

TBC


	5. Chapter 5

The Return Part 2: Favorite Son - Chapter 5

"Colonel?"

"Hmmm?"

"Colonel . . . John, are you all right?"

John wondered why anyone would ask that since he seemed to be drifting along, relaxed and comfortable. But the voice was familiar and seemed worried, so he focused on it, drawing closer and trying to answer.

"I'm 'kay," he slurred, his mind sluggish and slow. Blinking several times, he finally got his lids open and focused on the face in front of him. "Teyla?"

Teyla's expression relaxed a little as she smiled and nodded. "Yes, and Ronon is here too. Should we call Dr. Beck . . . the doctor?"

John's mind had finally begun to clear enough for him realize where he was. He had slumped over sideways so that his left side was leaned against the railing of the balcony, and he could feel the narrow metal pressing almost painfully against his arm and the side of his head. John yawned and struggled to sit up straighter. It was a bit of a battle since he was rather numb from the hips down.

"No, I'm okay, just dozed off I guess. What time is it?"

Teyla glanced up at Ronon and then back to John, irritating the pilot. "Hey, I'm fine. No silent conversations where you signal each other to call Beckett . . . or Emira, and tell them otherwise. I came out here for some fresh air and I guess I was more tired than I thought. I took a nap, simple as that. Beckett should be pleased." He delivered the last line with a small, but smug smile and a slight nod.

Ronon grinned. "So we should call him when he gets back and tell him about your nap?"

John narrowed his eyes at the Satedan. "Funny. Help me up. I think my butt is dead and my legs are completely numb. Was anyone going to tell me . . . never mind." John looked down at his watch as Ronon grabbed his hand and pulled him up. He'd been asleep over three hours. No wonder his lower anatomy was doing the pins and needles thing. He pumped his legs up and down as if walking in place, letting out a groan at the uncomfortable feeling of waking limbs.

"Well, this sucks. I should have just stayed in my room."

Teyla and Ronon were beginning to look amused. "We were just about to go to the mess hall for the evening meal. Perhaps you would like to join us," said Teyla.

John's stomach felt like an empty, gnawing pit. That was one question he didn't even have to think about. "Definitely. I think I missed lunch with all the getting released and touring my new room and everything. I'm starved."

John followed Ronon through the balcony door and into the corridor. "What have you two been up to all day? Did you have to go get your stuff as well?"

"No, we had already retrieved our things from the Athosian camp. Savill let us observe some of their training methods and offered to let us participate," explained Teyla. "It kept us much longer than expected. Several of the Ancestors were interested in the stick fighting, so after a demonstration, I taught them some basics."

"What about you, big guy?" asked John. "Did you . . . impress them?" John chuckled, remembering the looks Ronon always received the first time anyone saw him fight.

"Let's just say I didn't leave anyone standing."

"That's my boy," said John proudly.

Ronon grunted. "They were soft, even worse than your marines. They have depended on their technology too long."

"So . . . basically you guys got to kick butt all day while I was sleeping on a balcony because I was too zonked to walk twenty yards back to my quarters. There truly is no justice."

Teyla took John by the arm as they walked, squeezing it for a moment. "You were exhausted because of your efforts to save the Ancestors and the city. Only you could have operated the chair as you did so that we could defeat the Asurans. You have nothing to be ashamed of."

"Yeah, whatever," John drawled, but he squeezed Teyla's hand on his arm to let her know he appreciated her support. "You don't have to humor me, you know. My ego can take a little crushing." He sighed loudly. "It does every time you whip my ass at stick fighting or Ronon runs off and leaves me when we're training together."

"So, pretty much every day," added Ronon playfully.

John twisted his mouth in a look of distaste and did a quick head bob to the side. "Just for that, I'm not sharing my dessert."

"They don't usually have dessert," commented Ronon.

"Well, we'll have to talk to them about that," said John as they entered the mess hall.

They went to the counter, where plates were prepared by the time they arrived. They were all the same, no choices as when the people from Earth were in charge. A few minutes later, the three sat down at a table.

"I hope the food is good since there seems to be no choice in what we get," said John.

"Captain Helia informed us that this is not always the case. They are still making repairs to many parts of the city and food preparation is considered low priority for the time being," said Teyla.

John nodded. "Well, that's good to know. So, I'm curious. After spending the day with them, what is your take on the . . . Ancestors?"

Teyla and Ronon exchanged another glance, a habit they had fallen into a lot lately that was beginning to annoy John. "They are not as I expected," said Teyla.

John stilled, watching her expression for some hint of what she was thinking. "Care to elaborate?"

"There were very accommodating, but I felt as if . . . "

"They didn't exactly trust you?" finished John when she hesitated.

Teyla nodded, as did Ronon.

"Yeah, I've been getting that same vibe from Helia," commented John. "On the one hand, I can't blame her. She doesn't really know us, and even though we saved Atlantis, it's about as likely we saved it for us as for them. I probably wouldn't trust us either. Of course on the other hand . . . we saved Atlantis _and_ the Ancients. Why would we save them if we just wanted Atlantis for ourselves?"

"Because we needed them to defeat the Replicators," said Ronon.

John gave a reluctant nod. "Okay, I guess that's true. Maybe we should just give them some time."

"Do you trust them?" asked Ronon.

"Let's just say I don't distrust them, but I'm keeping an eye on the situation," said John carefully, remembering all of the times they had been stabbed in the back since coming to this galaxy.

"Hey, there you are! We've got stuff, lots of stuff!"

All three heads turned around to see Rodney leading the way across the mess hall with a smiling Elizabeth and Carson behind.

"Hey guys, welcome home," said John, surprised at the swell of emotion he felt seeing his friends return. He would never admit it out loud, but a small part of him had been afraid they wouldn't come back.

Rodney, Elizabeth, and Carson sat down at the table. "I see you got released," commented Rodney. "Been running or sparring yet?"

"Only with Ronon." John laughed when Carson's eyebrows shot up almost to his hairline.

"I'm kidding, Doc. I've had a very boring and easy day. I went to see my new quarters, visited the local balcony, and took a three hour nap. How's that for exciting?" He gave the most stern look he could muster to Ronon and Teyla, warning them not to reveal where he took the nap. They both smiled and looked quickly down at the table.

"A nap? Why Colonel, are you actually following doctor's orders this time around?" asked Carson.

John rubbed his chin and chewed his lower lip a second. "Didn't have much choice when I couldn't hold my eyes open. Any idea how long this whole tired all the time feeling will last?"

Carson smiled and gave a small chuckle. "Not long if you keep resting like you're supposed to, maybe a few days. How about the headache?"

John looked pleased at that question. "Almost gone, now that you mention it. That's good, right?"

"Aye, that it is."

"John, Helia had someone deliver your belongings to your room," said Elizabeth. "I understand it's next to mine."

John nodded. "Thanks. Yeah, the way I understand it, Ronon and Teyla are kind of across from one another, then Carson and Rodney. Across and down a bit is your room and then mine. Helia thought we could share the balcony."

Elizabeth nodded. "Well, we're used to sharing balcony time and space, so that shouldn't be a problem."

"Carson, did you get your turtles taken care of?" asked John.

"Aye, they were still alive, the poor little buggers. I took them back to the pet shop. He was very willing to take them back when I assured him I didn't need my money back."

John snorted. "Yeah, I'll bet. Well, I'm glad they were okay."

"Us too," said Rodney. "I was afraid we'd have to listen to him cry all day about those stupid turtles. Hey, I'm not sure if we got all your stuff or not. There didn't seem to be very much."

John nodded. "Thanks. I'm sure you got it all. When you spend your whole life moving around, you tend not to accumulate things. Makes it easier the next time you have to pack up."

Rodney looked dismayed. "But . . . that's all you have? That's all you own?" The shock and disbelief in his voice made John self-conscious and uneasy, as did the look of sadness on his face.

"Well, that's not _everything._ I have a few larger things, like a couple of pieces of furniture, in a mini-storage. I just haven't needed them in a while."

"But still, there was just a few uniforms and some clothes and –"

"McKay! Drop it. I don't collect things, okay. It's not important."

An uncomfortable silence followed, in which most of them stared at the table. Rodney finally cleared his throat. "Uh, we brought back some good stuff," he offered. "We have two coffee makers and a crate of coffee to share. And some chocolate and popcorn and other senseless, sugary snacks. Oh, and we got some new DVDs to watch as well."

"Sounds good," John said blandly. He felt like an idiot for snapping at Rodney and yet he just couldn't bring himself to apologize and chance the conversation going there again. While it was true he limited what he kept because he did move around a lot, he also knew that part of the problem was he had no one, and hadn't in a very long time. There were no keepsakes, no special gifts, and very little in the way of good memories. It was depressing, so he chose not to dwell on it and he wished they would do likewise.

"I have an idea," said Elizabeth. "We've had a busy day and wild week. Let's kick back tonight and watch a movie and eat some junk food. We can unpack tomorrow."

John smiled and began to relax again. He felt at ease with these people. Even tense moments seemed to pass rather quickly. It was the reason they were still together and back in Atlantis. They meshed on a plane he didn't pretend to understand. And that was okay, as long as it lasted. "Movie night sounds good. What did you guys bring?"

When his lop-sided grin came through, they knew the awkward moment had passed and they were back on track. Grinning, Rodney reached in his pocket and pulled out a piece of paper, carefully unfolding it. "Check this out!" he said proudly, laying it out on the table. Five heads immediately leaned over, trying to read the list at the same time.

oOo

The next two days went by slowly, especially for John. Teyla and Ronon were invited to train some of the Ancients in their style of fighting for several hours each day. It wasn't as exciting as missions through the gate, but it kept them occupied at least part of the time.

Carson was the busiest and most accepted, working with Emira in the infirmary to compare the two styles of diagnosing and treating patients. They also began examining Sheppard's medical records, comparing the results of different types of tests over a period of several years. He saw very little of the team during the day, usually joining them for the evening meal or shortly afterward if he and Emira had worked late.

Elizabeth was able to engage in several meetings with Helia and some of her diplomatic staff, updating them on the worlds they had visited and the enemies they had discovered. When she related the complicated history of their dealings with the Genii, she included their aborted attempt to take over the city. She made sure she included Rodney's plan to save the city using power from the lightning to provide energy for the shield and John's harrowing battle with the Genii forces. She thought they seemed suitably impressed.

Rodney was allowed to visit the labs and, of course, chose to visit the lab that used to be his. His stomach tightened and his jaw clenched upon entering, seeing others working at his old station. He had to choke back the demand that they all get out of his lab. Dolon introduced him to Renato, the lead scientist in that section.

Renato was a good three inches taller than Rodney and seemed to relish that he was looking down on the human scientist from Earth. He roughly explained some of the things they were working on in what Rodney found to be a very patronizing tone. When he was finished, Rodney very carefully pointed out that he could help him adjust for the power fluctuations they were experiencing as a result of the damage to some sections of the city. It was something the Earth scientist had to do often since it seemed they always had power problems.

Renato dismissed Rodney's offer as if refusing the suggestion of a six-year old on how to improve brain surgery. After another ten minutes of dropped hints and snide remarks by the physicist, Renato finally relented and agreed to let Rodney try. He was more than surprised when Rodney had the entire lab running at full power within two minutes. The other scientists came over to see who had fixed the problem, giving McKay his moment in the limelight.

John's day didn't go so well. He wandered around until he found where Ronon and Teyla were helping with the training. He arrived during a break and picked up a pair of sticks, twirling them around and savoring their weight in his hands. He itched to do something more than walk and nap, so when Teyla approached, he suggested they could do a demonstration together with some light sparring. Teyla looked at him like he'd lost his mind and then asked him if that was the case.

"It's just some light sparring. Or we could just do that Jung Shin thing if you want instead of the sparring."

"No. John, you are supposed to be resting. You may watch and that is all." Her voice was firm, her eyes unwavering.

"No thanks," he said glumly, casting his eyes down and pouting. And he knew he was pouting, he just couldn't seem to care enough to stop. Setting the sticks back down where he found them, he left the room.

Teyla watched him go as Ronon moved up beside her. "I should go talk to him," she said unsurely.

"No, let him go. He's just bored and feeling out of place. Neither of us do the sitting around thing very well. He'll be fine once the doctors clear him."

Teyla looked up at the Satedan. "And until then?"

Ronon grinned. "He'll just have to stay out of trouble."

"That's what worries me," said Teyla.

oOo

John noticed the guard at the edge of the control room come alert when he approached. "Sir, can I help you?"

The question caught John off guard, making him feel like he was trespassing in an area he was used to having free reign over. He hoped they started feeling more at home soon, because all this mistrust was making him wonder if he should have just returned to Earth. "I was just looking for Dr. Weir. I was told she was up here somewhere."

The guard seemed to relax a little. "Oh, yes, she's meeting with Captain Helia and Quies. Should I interrupt them?"

John sighed and scratched the back of his neck. "No, that's okay, it wasn't important. I just wanted to talk to her. You don't know where Dr. McKay is, do you?"

"I believe I heard Dolon say something about showing him some more of the labs."

John nodded. "Yeah, okay. Well, thanks." He turned and left the control room, wandering aimlessly down the halls for a while. He felt the familiar pull of Atlantis, and he smiled as he reached out to touch the wall. "I know girl. You're still here for me."

oOo

Helia watched as Elizabeth left the room and then walked out of her office to one of the sensor arrays. Aurigo, a young man compared to some of the others, was manning the console where they were keeping tabs on their guests.

"Aurigo, report on the location of our friends."

The slender man with short light hair nodded. "Yes, ma'am. Ronon and Teyla are still in the training rooms. Dr. Beckett is in the infirmary and Dr. McKay is in Renato's lab. Dr. Weir, of course, just left and appears to be heading for her quarters. Colonel Sheppard has been wandering around a lot. He was here earlier looking for Dr. Weir and in the training rooms before that. Since then, his movements have been very erratic, but now . . . Captain, he just entered the chair room."

oOo

John stood looking down at the chair. He hadn't intended to come here, he just had. Now that he was here, he longed to sit down and connect with Atlantis. He knew he was just depressed because he had nothing to do and it seemed everyone else had. He'd get over that when he was better. But it didn't make him feel any less lonely or useless at this moment in time. Licking his lips, he reasoned that surely just sitting in the chair couldn't hurt anything.

John sat down and felt the connection slide into place, warm and inviting. She welcomed him and he eased out a deep breath. She was already telling him about systems that were down and needed repair. It couldn't hurt just to scan for problems so he'd know what needed work. Maybe he could organize the repair work and send it to one of the Ancient terminals.

oOo

"Captain, he just activated the chair."

Helia spoke into her radio. "Savill, Colonel Sheppard has activated the chair. How close are you and your men?" Helia had contacted her security officer to take some men to the chair room as soon as she found out Sheppard was there.

"_Just around the corner. Hold on and I'll take a look."_

Helia looked anxiously over to Aurigo. "Has he done anything more?"

"No ma'am, so far he's just connected and seems to be . . . sitting there."

"_Okay, he's definitely in the chair and activated it, but I can't tell what he's doing. He's alone. Do you want me to remove him from the chair and take him into custody?"_

Helia paused only a moment. "No, not yet. I want to know what he's up to. Keep watch and let me know if you see anything unusual."

"_Understood. If he starts compromising systems, just let us know and we can have him out of that chair in seconds."_

"You'll be the first to know if we need him stopped." Helia stood beside Aurigo, watching the screen over his shoulder.

"Okay, he's doing something . . . He's . . . scanning the systems."

Helia tensed. "For weaknesses?"

Aurigo frowned and looked at her. "No, he's scanning for damage." He looked back at the screen, his frown deepening. "He's . . . ma'am, you aren't going to believe this. He's repairing the lighting in sector nine." His eyes studied the screen, his frown being slowly disappearing as his face relaxed. "Now he's restoring power to that area."

Helia was the one frowning now. "He's repairing the city? But why? How?"

Aurigo was now grinning as he worked the controls. "He's working with the city, almost like he's inside it ma'am. He's directing her systems and manipulating the automatic controls to take over when the repairs are completed. It's amazing. We've been trying to get the lights and power up in that sector for days now."

"Savill, just keep an eye on him, but don't interfere. He seems to be repairing parts of the city. Is he still just sitting in the chair?"

"_Yes, ma'am, still in the chair. He does have a rather odd smile on his face though."_

Helia was more confused than ever about this human's connection to Atlantis. She hated to admit it, but she felt a little jealous as well. Part of her wished she'd never invited Colonel Sheppard and his abilities to stay and yet part of her realized that he was probably the key to restoring the city.

"He's bringing up Sector 11," reported Aurigo.

Helia tensed once again. "There used to be some sensitive research going on in that area."

"It's okay, he isn't repairing that section. There's so much damage, we'll have to do some manual repairs before computers can be brought up and power restored. I think . . . wow, he is. He's sending an organized list of repairs and the sequence they should be done in, as well as parts that are needed. This should speed things up considerably."

Forty-five minutes after John powered the chair up, Helia received dual messages from Aurigo and Savill telling her that the chair had powered down.

"_He's just sitting there with his eyes closed. Should we go check on him?"_

"No, wait a minute and give him a chance first. If you go in there, he'll know we were watching him," said Helia.

"_Captain, I figure he already knows we're here. I would know we were here and the Colonel seems to be a decent soldier."_

"We cannot be certain that he is aware of your presence and he was preoccupied with the chair. Just wait."

"_He's trying to stand, so we're going to pull back." _Savill's voice was even softer than before, making him hard to hear.

"Watch him, make sure he gets back to his quarters," Helia whispered into the radio.

oOo

John was aware when the chair powered down, but he hadn't initiated it, Atlantis had. He had wondered why at the time, but now that the connection was broken and his head felt like someone had dropped an anvil on it, he thought he understood. She had known he'd had enough, even if he hadn't. She was protecting him.

And what was with the headache anyway? He sometimes got headaches after working with Atlantis for a while and he was usually tired, but not to this level. The concussion? Maybe a leftover effect of his power rerouting a few days ago. Either way, he needed to get back to his quarters before he passed out or threw up or both.

Standing was a bit of a chore, but staying upright when his balance went wonky was just as tricky. After swaying a few seconds, he simply plopped back down in the chair. He suddenly realized he was breathing too fast and probably hyperventilating, so he closed his eyes and made a focused effort to slow down his respirations. It took a few minutes, but his head finally cleared enough he could try standing again.

Slightly steadier on his feet, he managed to make it across the room where he could hang onto the wall. He began what seemed like an eternal journey to get back to his room. Fortunately, most of the way was relatively empty and he managed to look close enough to normal when he did pass anyone as to avoid raising suspicions. When he finally reached his room, he settled heavily on the edge of the bed.

His mistake was leaning over to untie his boots. John suddenly felt like someone being catapulted off a fast-moving merry-go-round. The sensation ended when he hit the floor, the jolt stirring up the pain and nausea. He lay there for a while, fading in and out as he tried to push away the encroaching darkness. Curling up in a partial fetal position, he managed to get his boots off. A few moments later, he used the bed covers to drag himself back up on the bed and lie down. His headache had reached migraine proportions and the light coming in around the make-shift curtains was too much. Pulling the blanket over his head, he burrowed down into the bed. When the darkness tried to roll in a few minutes later, he didn't fight it, welcoming the relief as it overcame him.

TBC


	6. Chapter 6

**NOTE: **Again, many thanks for all the reviews. You guys are so wonderful, you make me smile even on otherwise bad days (like yesterday). Hugs to you all!!

The Return Part 2: Favorite Son - Chapter 6

Carson carefully placed his tray on the table and then took a seat next to Rodney. "Sorry I'm late. Emira and I were just going over Colonel Sheppard's DNA studies."

Teyla and Elizabeth smiled at one another and Ronon snorted softly. Rodney paused to look at Carson almost like he hadn't seen him in a while. "So, you've been spending an awful lot of time with Emira. Is there something we should know about?"

Carson flushed and bowed his head, stirring the food on his plate with what passed for a fork furiously. "I have no idea what you're going on about, Rodney. Emira and I merely work together. We've just been going over all the Colonel's medical files and tests to see if we can figure out this Atlantis connection." As his face returned to its normal color, the doctor looked back up at his friends. "I have to admit, I've always been a bit curious, but never had the time to pursue it. Emira thinks it's a natural extension of my original work identifying the ATA gene. It's kind of nice to have the time for a little research again."

Rodney looked skeptical. "Research . . . right. And that's _all_ you're interested in?"

"Absolutely," said Carson. He looked around the room and then back to the others. "Speaking of the Colonel, did I miss him?"

Elizabeth shook her head. "No, I was just wondering where he was. I haven't seen him since this morning."

"We saw him earlier," offered Teyla. "He came to the training room to watch us for a while late this morning."

Carson stopped a bite midway to his mouth. "Only to watch?"

Teyla smiled. "That was all he did."

Ronon chuckled as he tore off a bite of some type of bread. "Not that he didn't try."

"Ronon," scolded Teyla.

"Ha! I knew he couldn't just do the rest thing very long," said Rodney smugly. "I'm guessing he wanted to stick fight."

Teyla glared at Ronon. "That was not necessary."

"Yes it was, lass," said Carson. "It tells me the Colonel was bored and willing to disobey his instructions in order to entertain himself. Which means if he doesn't show up soon, we'll have cause to worry. I wonder what he's bloody well gotten himself into this time."

They continued to talk as they ate for the several minutes, each of them periodically glancing toward the door. As they neared the end of their meal with no sign of Sheppard, the conversation began to die down and they began to worry in earnest. One by one, they noticed the Ancient Savill making his way toward their table.

"Good evening. I hope you are enjoying the meal."

Elizabeth smiled. "Yes, very much so, thank you."

Savill looked around the table and frowned slightly. "I notice Colonel Sheppard is not with you this evening. Do you know where he is?"

"Actually, we were just discussing that," said Rodney. "We're not exactly sure where he is. Have you seen him?"

"No," Savill lied smoothly. "I just wanted to ask him something. Several areas with damage began to repair themselves early this afternoon and the control room received some repair lists on other areas. These were sections we either don't have scheduled to look at for a while or we have had trouble with. I have heard of the Colonel's connection to the city and I thought perhaps he had something to do with it. I thought maybe we should offer our thanks."

The group went silent for a moment, then Rodney and Carson made eye contact. "Colonel Sheppard," said Carson, sighing as he shook his head.

"He sat in the chair," said Rodney.

"We should check on him," added Teyla.

They all stood hurriedly, the level of worry increasing dramatically. Elizabeth turned to Savill. "Thank you for stopping by, but we really need to go check on Colonel Sheppard."

"I told him not to go near that thing until I had cleared him," said Carson angrily, slamming the chair into the table as he pushed it up.

Savill almost smiled. "I'm thinking maybe I just got Colonel Sheppard in trouble and that was not my intention."

Elizabeth nodded. "Oh, he's in trouble all right. I just hope he's okay. The fact that he didn't come to dinner would seem to indicate otherwise, however. Thank you for stopping by, but I'm afraid we need to go now." Elizabeth was watching the others head for the door without her.

"Yes, I can see that. Please let us know if we can help."

"I will and thank you again." Elizabeth turned and hurried to catch the group as they disappeared out the door.

Savill watched them go and relaxed a little. He'd followed Sheppard all the way back to his quarters and he hadn't been entirely sure the man would make it. Checking with Aurigo at the control center, he'd discovered that Sheppard hadn't left his room the rest of the day. Knowing the group of humans usually ate their evening meal together, he'd watched to see if the missing Colonel would show up. When he hadn't, Savill had been worried the time in the chair had hurt the Colonel and sought a way to motivate his friends to check on him. He smiled now, sure that they would see to it Sheppard was taken care of. He found himself beginning to like and respect the man.

oOo

"Should we check the chair room or his quarters first?" asked Rodney as they moved down the hall.

"His quarters are closer," said Carson. "I'm going to swing by my room and pick up my bag and then I'll meet you there."

When they reached the corridor with their rooms, everyone stopped at John's door except Carson, who continued past. Rodney knocked loudly several times. "Sheppard, open up." He immediately knocked again.

"Open it," said Elizabeth.

Rodney tried the door controls, hoping Sheppard hadn't locked it. He was relieved when it slid open to reveal the dark interior. They stepped inside slowly, letting their eyes adjust to the change. Squinting, Rodney was finally able to see well enough to tell Sheppard was curled up under the blankets. "He's here."

They had only taken a few steps inside when Carson entered, carrying his medical bag. He was barely in the door when Rodney turned the lights up enough for them to see. The doctor went immediately to the bed and sat on the edge. The Colonel was completely hidden, the blanket pulled up over his head. Carson reached out to gently shake the man's shoulder. When he got no response, he nudged Sheppard a little harder.

"Whaaaa, sssstop," came the muffled plea from under the covers. The lump in the bed shifted and then went still. Slowly a small hole appeared at the apex of the cocoon.

Carson found himself peering down into a dark tunnel at one glaring, partially open eye and half a face, along with a tuft of dark hair. The one visible eyebrow creased and the doctor could almost picture the frown appearing on the full face of the pilot. Sheppard shifted so that the hole closed. "Lights."

Carson was about to tell Rodney to turn down the lights when they dimmed automatically. They all looked around the room and then back to the bed.

"So is Colonel Lump coming out anytime soon?" asked Rodney.

"No," said the mass under the covers. "Go-way."

Carson sighed and shook his head. "I'm afraid we can't do that, Colonel. We have a wee bit of a problem. Someone's been repairing Atlantis from the chair they were told not to go anywhere near. Would you know anything about that?"

The form shifted and the hole reappeared, along with the half face and one glaring eye. "How'd you know?"

Elizabeth stepped forward, her posture a bit more relaxed than when they had first entered the room. "Savill was asking about you. He said someone had been fixing the city and he wondered if it was you."

John snorted and then moaned with regret, the painful kind. The sound seemed to echo loudly around in his head. He didn't realize he'd closed his eyes against the pain until he opened them again.

"Colonel, are you all right?" asked Carson worriedly.

"Headache," John whispered.

"Aye, I thought as much. And light sensitive too. Let me check a few things and maybe I can get you something for that."

John narrowed his eyes at the doctor, not realizing only one was visible. "No infirmary?"

Carson looked at the man thoughtfully. "Not if you check out okay. I need to see more than one eye and half your face though."

John studied the lighting and decided it was dark enough. He squirmed a bit to get the blanket pulled down to his waist since he was wrapped up in it. When he was finally settled again, Carson began strapping on the blood pressure cuff.

"I'm glad Savell asked about you, John. We missed you at supper, but we wouldn't have known what was wrong if he hadn't told us about the repairs," said Elizabeth.

"Rat," muttered John.

"Savill merely wanted to find out if you were responsible so he could thank you," said Teyla.

John grunted. "He knew it was me. He was watching me from the hall, along with what sounded like a couple of teams. Well, him or one of his men. He wanted to turn me in."

The others stiffened. "He . . . he was watching you?" asked Rodney nervously.

"Yeah, they appeared just a few minutes after I activated the chair. I think someone was keeping tabs on me to know what I was doing that quickly. I'm getting the distinct impression our hosts don't trust us." John absently rubbed his head, willing the throbbing to stop.

Carson prodded the Colonel. "I need you to sit up if you can and stop talking."

John didn't answer, but began trying to sit up. Carson got one hand on his back and helped him until he was sitting hunched over in the bed, one hand fisted around the blanket.

Carson steadied John with a hand on his shoulder. "Colonel?" A thin sheen of sweat was beginning to form on his patient's forehead. "Teyla, could you get me a damp cloth please?"

John swallowed carefully, pushing back the nausea that had accompanied the explosion of pain in his head from being vertical. He zoned out for a moment, lost in trying to work through his misery until it subsided enough for him to function again. The background noise began to clear up enough for him to realize Carson was talking to him. Hands on his shoulders guided him back to being horizontal again and he felt a welcome coolness across his face.

"That's it Colonel, just breathe deeply and try to relax."

The sharpness of the pain and the nausea both began to ease so that John opened his eyes again. Teyla was wiping a cloth across his face and smiled down at him. He gave a tiny nod, the most movement he was willing to risk. "Thanks," he said softly. "Better now." He shifted his gaze to a worried looking Carson, noticing the rest of his team didn't look very happy either.

"Colonel, I don't know. Maybe we should get you back to the infirmary."

"No . . . just need . . . sleep." Exhaustion was settling back in, warring with the pain for his attention.

Carson finally gave a small nod. "Your blood pressure is a bit low, but other than that, everything else checks out okay. I'm going to give you something for the headache so you can get some sleep. I don't want you to leave this room until I've checked on you tomorrow and I'm not kidding about that. If I find out you went around me again, I'll confine you to the infirmary until you have completely recovered. Do I make myself clear?"

"Crystal," said John. He didn't care, he just wanted the pain to go away. He'd worry about the lecture and how much trouble he was in tomorrow. He drifted for a few seconds as Carson dug around in his bag and then jumped slightly at the cold alcohol wipe on his arm. A small sting just after that let him know Carson was giving him something strong, and for that he was grateful. He forced his lids open part way so he could look at the doctor. "Thanks," he mumbled.

"You're welcome," said Carson simply before packing his stuff back into his bag.

"Is Sheppard okay?" asked Ronon.

Carson stood up and set the bag on a table. "Yes, I think so. He's exhausted himself again. I think using the chair right now, while the city is damaged and still suffering the effects of the Asurans, is giving him problems. I don't even know how he operates it so deeply, so there's no way to fully understand what it's doing to him. He won't like it, but I may haul him down to the infirmary for a scan when he feels better."

Ronon nodded. "If he argues, I'll carry him down there."

Carson chuckled, entertained by Ronon's version of helping, although sometimes brute force did come in handy. "Well, I'll keep that in mind, but I don't think he'll protest that much."

"Not if you promise to let him come back here afterward," said Elizabeth.

"Aye, you're right about that. The lad doesn't like being confined there. Can't blame him really. Not a lick of privacy." He looked back around at his sleeping patient. John rolled over on his side and pulled the blanket back up over his head, groaning slightly as he moved.

"I think everyone should get out of here and let the Colonel get some sleep," said the doctor firmly.

They all glanced at Sheppard before turning and making their way to the other side of the room. As the door slid open, Elizabeth turned around to see Carson still standing beside the little table. "Carson, are you coming?"

Carson watched Sheppard for a few moments and then twisted back around to face the group. "I think I'll sit with him for a while, just to be sure."

"I'll relieve you about ten," said Rodney.

"Then I will come at one," said Teyla.

"That leaves me at four," said Ronon.

Elizabeth's gaze went from one team member to the other as they chimed in claiming their watch. "It would appear you have lots of experience at this."

Rodney smirked. "Way too much, trust me. See you at ten."

Elizabeth glanced back at Carson, who was smiling as they began to file out of the room. Teyla gave her a small nod as they walked out together and closed the door. She headed for her room, thinking she might read for a bit, when she met Helia walking her way.

"Helia, hello."

"Good evening, Dr. Weir. I saw Savill a few minutes ago and he told me about Colonel Sheppard. Did you find him?"

"Yes, we did. He was in his quarters."

Helia nodded. "He is all right then."

Elizabeth nodded toward her door, just a few feet away. "Would you like to come in for a moment? There's something I'd like to discuss with you."

Helia looked surprised and took a deep breath, obviously unsure of what to do. After a moment, she pursed her lips and nodded. "All right, Dr. Weir, I can do that."

"I was just going to make some coffee. When it's finished, I'd love for you to have a cup with me," Elizabeth said as they entered her room. She went to the coffee maker and began preparing it. After their two and a half year stay, Rodney had quickly adapted the appliance to work with the power in Atlantis.

"We'll see. You didn't answer me about Colonel Sheppard."

Elizabeth turned the coffee maker on and then sat down at the small table with her guest. "John will be fine, we think. Right now, he's exhausted and has a rather severe headache, but Carson thinks he'll be okay with some sleep. He told us a little while Carson was examining him. He did activate the chair and begin repairing parts of the city. I hope you don't think he was trying to do anything behind your back, he just has this need to be doing something and he has a hard time following doctor's orders, especially when they are to rest and do nothing."

Helia relaxed a little and nodded. "I do understand that, as some of my people are the same way. But as the leader of this city, he needs to check with me before doing anything with or to the city, especially anything involving the chair controls. I'm sure you, of all people, can respect that I must remain firm on that position."

Elizabeth frowned slightly. "I understand that you must be careful and I even understand your stipulating that level of control, but I just need you to try and see John's point of view. We thought you were gone, all of you. For well over two years, this has been our city, she's been his city in particular. He says he felt her from the moment we arrived, he just didn't understand it for what it was. He feels connected to her on some level every minute he's in the city. And I've come to believe that the city feels him and loves him back on some level. John would never do anything to hurt her. He came all this way and risked his life to save her. He's trying to protect her."

Helia looked at Elizabeth for a long minute, making Elizabeth more than just a little nervous. "I tend to believe you, Dr. Weir, I really do. You seem to be good people and you've given us no reason to mistrust you so far. I just have to take certain precautions until we know you better, until I can be certain."

"Certain of what? What is it you think we're going to do? Take over the city for Earth? You know we don't have the best relationship with them when it comes to Atlantis. And that trouble is born from the love we have for the city and for what it represents." Elizabeth sobered her expression. "So were you having John watched directly or keeping up with him on the sensors?"

The question caught Helia off guard. "I'm not sure what you mean."

"John told us there were people in the hall keeping him under surveillance within a few minutes of him activating the chair."

Helia's expression mirrored the conflict going through her head. She started to speak and then stopped, then started again. "We've been monitoring all of you from the security screen. I just felt it was best until we were sure of your intentions."

Elizabeth nodded. "We've suspected you didn't trust us, I guess we just didn't realize to what extent. We saved your lives and then your city. We willing handed it over to your control twice now. If you still don't trust us, I think it's safe to say you probably never will. I'll talk to the others tomorrow, after John gets up and about, to see what our options are. As we say on Earth, I think we may have worn out our welcome."

Helia looked down at the floor, frowning deeply. "I did not intend for this to happen. We would still like for you to stay."

Elizabeth stood. "We have another saying on Earth. Actions speak louder than words. Would you like that cup of coffee?"

Helia also stood and brought her eyes up to meet Elizabeth's. "I think perhaps another time. I think I understand the phrase about wearing out your welcome."

Elizabeth followed her to the door and opened it. Helia stepped out into the hall and turned back to face the woman from Earth. "I hope Colonel Sheppard recovers all right. I'll speak with you tomorrow."

Elizabeth nodded and closed the door, walking slowly over to the coffee pot. She poured herself a cup and stood looking at the door while another saying came to mind. "Don't let the door hit you in the butt on your way out," she said, smiling sadly.

oOo

Helia walked into her office and sat down, lightly chewing her lower lip. A noise at the door caused her to look up a few minutes later.

"Did you talk to them?" asked Savill, standing just inside the door way.

"Yes, I talked to Dr. Weir as they left Colonel Sheppard's quarters."

"Is he all right?"

Helia looked up at her second in command and frowned. "You seem overly concerned for the Colonel."

Savill shrugged his shoulders. "No, just curious. Sheppard seems like a good man and I would hate for him to get seriously hurt."

"He's got a headache, but it looks like he'll be fine. I think I may have pushed them a little too hard. Sheppard knew you were there."

Savill grinned, but didn't say anything. Helia finally gave a small smile and looked up at him. "Yes, I know, just like you told me."

Savill nodded. "I told you, Captain, he's a good soldier. We need them to stay, I can feel it. There's the obvious reasons. Sheppard's connection to the city can be invaluable helping us repair and run it to its full potential. McKay has already impressed some of the scientists and we can definitely use another good healer. Sheppard, Ronon, and Teyla are all good soldiers on several different levels. Sheppard is smart, dangerous smart. Have you heard about when the Genii invaded the city?"

"Yes, Dr. Weir filled us in the other day."

Savill narrowed his eyes at his commander. "If Sheppard wanted to pull something, he'd have done it by now. You saw what he did to the Asurans. I can tell you from the little I've seen and heard that you want that man on your side. I know soldiers. I understand he's also an excellent pilot and we're short on those."

Helia leaned back in her chair and smiled mischievously. "You really do want them to stay, don't you?"

Savill sighed and scratched his neck. "Yes, I do. And it's more than just the logic of it, it's also a gut feeling that we need them. I can't fully explain it."

Helia's expression slowly became more serious. "You're connection to Atlantis is fairly strong compared to some of us. Could she be influencing you?"

Savill snorted. "How is that possible? Atlantis is a city."

"Dr. Weir seems to think Atlantis likes Colonel Sheppard, a lot. And I've heard similar comments from some of the others. Maybe she's trying to tell us she wants him here."

Savill shrugged his shoulders again. "I don't know about that, but I know we need them here and I think we can trust them. If they're going to stay and actually be of value, you'll have to start trusting them sometime."

Helia nodded. Although she could see positive contributions possible from all of them, she was still somewhat fixated on Sheppard's connection to Atlantis. It was the key to restoring Atlantis and defending her. "I know. I just hope it isn't already too late."


	7. Chapter 7

**NOTE: **Thanks again for the encouragement. I've been trying to post this chapter for several days, but Fanfiction wouldn't let me. It just kept telling me there was an error. Today I'm trying something new to see if I can trick it. Anyway, I'm sorry for the delay and I hope you continue to enjoy.

The Return Part 2: Favorite Son - Chapter 7 

John groaned as he rolled over to his back, aching muscles protesting the movement. Settling, the discomfort did not abate and a throbbing at the base of his skull began to build. After a few minutes, he was convinced that going back to sleep did not seem to be a viable option. He tried to push the covers down, but found himself wound too tightly in the blankets to get his arms free. When he began struggling in earnest, he was startled to discover that even his head was covered. Twisting in such a way as to free his arms from their unintentional bindings, he groaned again at the dull pain it caused.

Flopping the covers out and away from him, he took in a deep breath of fresh air and sat up. When the headache spread quickly up behind his eyes, he decided that sitting up that soon probably hadn't been the best plan.

"Nice hair."

The insult didn't even register as John blinked sleepily several times to clear the fog. Unfortunately, the action didn't help the way his mind seemed to be moving in slow motion, like someone trekking through deep mud. He slowly took in the room, noticing that his whole team was there plus Carson and Elizabeth.

"What's up? You guys just watching me sleep?" he asked slowly, almost like he was drugged. He felt like something had happened, but he couldn't seem to get a grasp on what.

Rodney smirked as he exchanged a look with Carson. "Oh, yeah, that's it. And later this afternoon we're going to ask if we can go to the mainland and watch grass grow."

John just looked at him, too confused to think of a comeback. He couldn't get his thoughts going and he was still so tired. He rubbed one hand through his hair and yawned. "Why are you here?"

Elizabeth walked a few steps to stand by the bed. "We were getting worried. You've been sleeping almost twenty-four hours."

John was speechless, wondering how he could have slept so much and still feel like his body was made of lead, eyelids included. "Straight?"

Rodney grinned. "Well, you did stagger to the bathroom a couple of times, but you didn't really seem to be what I'd call awake. It's a wonder you managed to aim, as out of it as you were."

John just looked at him blankly, not remembering any of it. "Oh." He looked down at the bed, trying to remember what had happened to make him feel like crap and get his team worried enough to sit with him. He startled at the touch of a hand on his arm. He realized he must have zoned out or dozed off because Carson was sitting on the bed beside him taking his pulse.

"Sorry, lad, didn't mean to startle you."

John nodded. "Guess I'm still kind of out of it."

Carson set his arm back down, apparently satisfied. John watched as the doctor took his blood pressure and temperature and then listened to his heart and lungs. He didn't say a word of protest until the pen light came out.

"Doc? Is that necessary?"

Carson seemed to study his face. "Still have that headache?"

"Uh, yeah." The throbbing had settled in behind his eyeballs and running down to the base of his skull and into his neck. He suddenly remembered sitting in the chair and connecting with Atlantis. Carson held his chin still and flashed the light in his right eye, sending a sharp pain stabbing through it. John tried hard not to flinch, but in the end, he twisted his head away.

Carson sighed as John rubbed his eyes, remnant light images spotting the inside of his lids. "Colonel, I need to see the other eye."

" Carson, it hurts," John complained. He felt like a whiny kid who didn't want his shot, but the previously manageable headache had just about doubled in intensity. He didn't really want it tripled.

"I know, lad, but I need to see your pupil reactions. I'll be quick."

"Come on, Sheppard, suck it up," said Rodney from across the room.

"Rodney, that was unnecessary," scolded Teyla. "The Colonel does not complain about pain unless it is substantial."

"Yeah," added Ronon. "Unlike some people."

"Oh, and I suppose that's supposed to be a dig at me. I'll have you know I don't complain about pain unless it's a lot of pain . . . and life threatening . . . and really . . . dangerous."

Everyone stared at the scientist until he finally blew out a puff of air. "What?" he said sharply.

Carson turned back to John. "Colonel?"

John gave in. "Fine." He tried to hold still as Carson once again held his chin and flicked the light into his left eye. This time instead of pulling away, he settled for just slamming his eyes shut, feeling them water slightly at the sharp pain.

Carson made a "Hmmm," sound as he stood and put his instruments into his bag.

"So, what's hmm mean?" asked John, still rubbing his closed lids. 

Carson turned back to his patient and crossed his arms. "It means your heart and blood pressure are all right, but you're pupil reactions are sluggish and slightly unequal. Does one side hurt more than the other?"

John thought about it a few seconds. "Right side is a little worse."

Carson nodded. "Thought so. Now, would you mind telling me what you were doing in that chair even though I told you specifically not to go there?"

Although he still felt like his mind was mush, he had remembered what had happened. He looked down at his hands in his lap, knowing he really didn't have a good excuse. "I don't know. I didn't go there intentionally, I just sort of ended up there. And then . . . I just wanted to sit down and, you know, be close to her. I just wanted to feel her and know she was there. But then damage reports started cropping up and I felt like she wanted me to help her and . . . I guess I wasn't really thinking at that point."

"No, I guess not, because anyone with any thinking skills at all would have remembered that this is the kind of thing that got you in the infirmary in the first place and would have walked away."

John worked up his nerve to look up and make eye contact with the doctor. "I'm sorry, doc." And he was. He knew it had been stupid, that the damage wasn't anything critical that needed to be fixed in a rush.

Carson sighed and gave a small smile. "I know, Colonel. And I know you were only trying to help, but you've got to be more careful. Now, are you hungry?"

John was hungry, but not starving like he thought he should be. The headache was probably responsible for that. "Sort of."

"I'll get you something for the headache and Teyla, will you see about getting the Colonel some food?"

Teyla nodded and immediately headed out the door. John rubbed his eyes and scooted around so that his legs hung over the side of the bed.

"Going somewhere?" asked Carson.

John knew better than to nod. "Yeah, the bathroom, unless I have a catheter and I'm so out of it I missed that fact." As he stood, Carson took hold of his arm to help him up. John did't argue against the steadying hand until they reached the bathroom door. "I've got it the rest of the way," he insisted.

Elizabeth watched as the door closed and Carson turned around. "Is he okay?"

"Aye, I think so. He just needs some food and a bit more rest. I would like to take him down to the infirmary for a scan after he eats though, just to be sure. I've already cleared it with Emira."

Elizabeth nodded. "I think I would feel better as well. He's too quiet and too still."

Carson chuckled. "Aye, I know what you mean. He usually puts up more of a fight than that."

When John went to wash his hands, he caught sight of his refection in the mirror. He was surprised at how pale he looked, with dark shadows under his eyes making him look ill and sleep deprived. He rubbed the stubble on his chin, thinking that the lack of shaving didn't help any. He started to look away and then noticed his hair. It was sticking out in all directions, from the top, sides, and even in the front. At least he understood Rodney's comment now. He dampened his hands and ran his fingers through his hair a few times, getting enough of it to lay down he looked a little less like someone who had been recently electrocuted.

He was about to turn around when someone knocked loudly on the door. "Colonel, are you all right?"

John sighed as he stepped toward the door and opened it to find Carson standing just outside. "I'm fine Dr. WorryWart."

Carson crinkled his face. "Cheeky. Have a seat at the table. Teyla should be back with your food in a minute."

John shuffled over to the small table and sat down in the empty chair, stifling a yawn. Carson set two Tylenol and a bottle of water in front of him. "Thanks," he said as he picked them up.

"What, no Dr. WorryWart?"

John smiled as the set the water bottle back on the table. "Sorry about that." He glanced at Elizabeth, sitting next to him and she winked at him.

The door opened, drawing everyone's attention as Teyla came in with a tray of food. She quickly set it in front of John and then took the seat across from him. "I hope this is all right. Since it is between meal hours, they had to make something. I directed them in making a sandwich and they had something similar to a fruit bar."

John gave one short nod. "It's fine, Teyla, thanks." He took a tentative bite of the sandwich and chewed slowly for a few seconds. "Not bad. I guess you gave them good instructions."

"I was happy to help, John. How are you feeling?"

John swallowed his latest bite and washed it down with some water. "I'm okay. A little tired, still have a bit of headache."

Rodney, Ronon, and Carson pulled up chairs to all sit in a wide circle around the table. John frowned as he watched the movement. "Okay, first of all, where did all these chairs come from? And second, what's going on? I know you people aren't hanging around to see me eat a sandwich."

Elizabeth cleared her throat and looked up at him. "We brought some extra chairs from our quarters so we could all sit. We need to talk, all of us. I talked with Helia yesterday, after we found you here in your room. She's been keeping tabs on all of us since we got here, watching our movements on sensors."

John sighed and set his sandwich down, looking blankly at his plate for a moment. "I knew she didn't trust us and I thought she was keeping tabs on me, but I didn't know she was watching all of us."

"Kind of creepy, huh," commented Rodney.

"Yeah," agreed John. "I guess she was upset about me using the chair."

Elizabeth widened her eyes for just a second. "She wasn't happy that you did it without her knowledge or permission. I think she's a little afraid of you."

"Aren't we all," said Rodney.

"Funny," said John. He leaned forward and rubbed his eyes and then his forehead, wishing the Tylenol would kick in. "So what else did you talk about?"

"Trust. I told her if they were that distrustful of us after everything we've done and sacrificed to be here, then maybe we didn't belong here. That's what we need to talk about. If they aren't going to trust us, to let us help and do what we're capable of, then maybe we should just go home. I need to know what you guys think."

Ronon looked at Teyla, who nodded, and then turned to the rest of them. "Teyla and I have been talking. It's been interesting training the Ancestors and working with them, but it's not like going through the gate and fighting the Wraith. It kept us occupied for a while, but it isn't doing anything, not really. We feel useless like this. We've . . . been talking about returning to her people and then figuring out a way to be more active in the fight."

Rodney nodded. "I know what you mean about feeling useless. While I was allowed to visit the labs and I ended up fixing a small power problem for them, they wouldn't let me touch anything else and basically acted like I was too stupid to be there. I stood there and figured out how to solve two of their problems from across the room, but they wouldn't listen to me. I don't want to leave Atlantis, but if all we're allowed to do is look from across the room, I don't see much point in staying."

" Carson?" said Elizabeth.

Carson looked thoughtful for a few moments before answering. "I have mixed emotions on the matter. I've enjoyed working with Emira and it's been nice to be doing research again. But my only patient is Colonel Sheppard and I have to admit to rather missing being a practicing physician. I feel like I'm shirking my duty somewhat. I'd be happy doing what I'm doing for a while longer, but eventually, I think I'd get tired of just doing research and I get the impression that the people in this room would be my only patients."

Elizabeth nodded and turned to the man sitting next to her, his face strained with pain and exhaustion. "John, what about you?"

John kneaded his neck and the base of his skull. "I don't know if I can leave." He looked up at his friends and wondered if he'd be able to make them understand. "I feel the same way about sitting around and being useless, I think you guys know that. But . . . I need Atlantis and she needs me."

"What, is she your newest girlfriend?" asked Rodney sharply.

"No, it's not like that," John said evenly. "I'm drawn to her, to the feeling of her being around, sort of like a child craves having their mother around. But then I think she needs me too, kind of like the roles are reversed and I'm the parent. When we were back on Earth, I didn't feel right, like something huge was missing. I felt off, almost disoriented sometimes. I need to be near her on a regular basis."

"What, like a drug addict needed drugs?" asked Rodney, looking both amazed and worried.

"No . . . yes . . . well, maybe sort of. I don't know how to explain it and it's been even more intense since we returned. I think it's become almost a physical . . . not really a need, but more than an attraction. I don't want to be stuck here being watched while I do nothing, but I'm just not sure I can go back to Earth without . . . losing it."

"And then there's Landry to consider," said Rodney thoughtfully. "If you go back to Earth, Helia'll be pissed because she wants you and your gene to stay here. If she let you go back at all, she'd probably cut off all relations as payback and then the government would be upset."

John gave a small nod, still hurting enough to mute his movements. "Worse case scenario is prison for me, best case is a dishonorable discharge or an assignment somewhere more remote than Antarctica."

"Is that even possible?" asked Rodney.

"You'd be surprised at what's possible. What about you?" asked John, looking at Elizabeth.

Elizabeth sat looking down a few moments before answering. "I also have mixed emotions. Like the rest of you, I'm feeling useless and spied on, yet I love this city. Life on Earth was just . . . not the same. I missed her, even though I don't have the gene and the connection John does. There's something very magical about this place."

"So, we've decided that we all want to stay but we don't want to sit around doing nothing and if we do stay, they'll only let us sit around and do nothing. Hasn't this been a profitable meeting," complained Rodney.

A sudden knock at the door startled them all. Ronon quickly got up and opened the door. He stepped aside to allow Helia to enter the room.

"Good, I'm glad you're all here."

"Like you didn't already know that," muttered Rodney.

Helia pursed her lips and gave a short nod. "I suppose I deserved that. I'd like to talk to you all, if I may."

Elizabeth looked at the others and then nodded. "All right."

Helia took a deep breath. "I've been thinking about what you said, about trust. And Savill, my second in command sort of agrees with you and I trust his judgment. I wasn't acting out of malice toward you, I was just being cautious. But I was thinking about how I would feel in your position and . . . I decided I'd be at least as upset as you are."

"So does that mean you'll trust us from now on or that you're kicking us out?" asked Rodney acidly.

"Rodney!" Elizabeth scolded.

Helia smiled. "It's all right, Dr. McKay speaks his mind. I can respect that, even if it isn't always what I want to hear. I want us to try this again. I've already stopped the surveillance and it will not resume unless you do something to arouse suspicion. Dr. McKay, I think we've been underestimating your use. One of Renato's assistants told me about you solving their energy problems so quickly when you were there."

Rodney smiled proudly. "Yes, well, that was easy as we were always having power problems. I could have repaired some other things as well, but Renato didn't want me to touch anything."

Helia let out a small sigh. "I've been considering something. We were a war ship and most of the scientists we had on board were there to keep things running smoothly and solve problems that occurred. They weren't really experienced research scientists. Most of those were in Atlantis until it was evacuated. I think Renato feels threatened by your presence."

Rodney almost seemed to puff up with pride. "Well, I can see how that would happen. I am, after all, a genius."

Teyla sighed, Ronon snorted, and Carson rolled his eyes. Elizabeth and John just exchanged a glance and then looked back at Helia, whose expression remained diplomatically neutral.

"Yes, so I've heard. If you decide to stay, I would like to offer you a position in the lab. I think it might be prudent if you reported directly to me instead of Renato. There are two scientists who have expressed interest in working under you."

"They obviously don't know him very well," said Ronon.

"Look, Conan, no one asked you," said Rodney.

Helia turned to Carson. "As for you Dr. Beckett, Emira has been very impressed with your abilities and we've seen how dedicated you are to your patients. She has offered to train you in the use of any devices you are unfamiliar with and make sure your methods of treating wounded are up to our standards. As she decides, you will be allowed to take on patients of your own or help with emergencies, as well as continue your research."

"And Dr. Weir, I have learned from our conversations that you possess great leadership and diplomatic skills. If you are interested, I'd like for you to meet with all the allies you have made and act as negotiator between them and us. We have some worlds in our database that you have not explored and I'd like to put you in charge of scheduling their exploration and negotiating with anyone that you find."

Elizabeth frowned a little. "You want _me_ to handle negotiations with new worlds?"

"Yes. We do not have enough people to work on negotiations with other worlds, and yet there are things we need. Most of my people are engaged in running and repairing the city. We were meant to man a ship, not a city. When I took a step back and looked at the situation realistically, I began to realize just how much we needed you."

Helia shifted her gaze to John. "Colonel Sheppard, as soon as you have recovered, I'd like you and Ronon and Teyla to get back to work as a gate team, doing things very similar to the way you did them before we returned. You would work with Dr. Weir to explore new places and renew existing friendships. We will need some food sources to supplement what we are capable of producing in the city, as well as information about the Wraith and other potential enemies. You will report to Dr. Weir, who will in turn report to me."

The humans were shocked, not having expected the generous offer. Elizabeth finally shook herself out of her daze and stood, looking at Helia. "This is . . . a very generous and unexpected offer. Could we have a few minutes to talk about it?"

Helia nodded. "Yes, of course. I expected you would need to do so. I'll return to my office and you can let me know of your decision. While I will not apologize for being cautious, I will say I'm sorry for the hurt it caused and perhaps for not making myself clearer. I hope that we can build a strong relationship from here and become allies."

John looked up at Helia and frowned. "What about the gene thing, my connection to Atlantis?"

Helia looked as if she had been expecting the question. "You can be very valuable in helping repair the city and in taking control of certain systems during times of crises. I would still like to understand more about your connection, but I will not force anything on you. It will be your decision."

"Well, he'll not be helping with the repairs, at least not from the chair, until we can assure it won't affect him like this," said Carson.

" Carson, there may be some things they really need me for," said John. "If I can help Atlantis, I'm going to."

"Wait a minute," said Rodney. "Before you two get into another snit, I have an idea what may be causing that. Sheppard, you won't be in any shape to do anything for several days and I can probably have it figured out by then."

"Fine, see that you do," said Carson.

"Well, I think some people may have already made up their mind," said Elizabeth smiling, "but I'd still like a chance for all of us to discuss the offer."

Helia nodded. "I understand. I'll be in my office when you're ready." With a small nod, she turned and left.

Rodney grinned. "Everyone who wants to stay and try this, raise your hand." Rodney raised his hand immediately, followed one by one by the others.

Elizabeth snorted. "Well, I actually had a more involved discussion in mind, but I guess this will do. Everyone seems pretty certain."

"That's because we never really wanted to leave in the first place," said John, leaning his chin into his hand, his elbow propped up on the table.

Carson looked down at John, noticing the drooping eyelids and lines of pain. "I think I need to get the Colonel down to the infirmary before he drops off again."

John jerked his head up, wincing and rubbing his forehead at the surge of pain. "Infirmary?"

Carson fought not to laugh. "Just for a quick scan and then you can come right back here. Emira's waiting on us."

John groaned, not sure he had the strength to walk all the way to the infirmary. He knew he didn't have the desire. "How about later?"

"Now, Colonel. If you can't make it, I'll call for a wheelchair . . . or a gurney."

John sighed and struggled to his feet. "I'm coming, I can walk."

"The question is how far?" said Ronon.

John grunted with effort and annoyance as he toddled to the door. "Nice. You're starting to sound like McKay."

Ronon narrowed his eyes and crossed his arms. "Just wait until you're back up to sparring strength, Sheppard. You'll pay for that one."

Carson took Sheppard by the arm to help support and guide him. "Come on, Colonel, let's get you out of here before you get yourself into any more trouble. You've spent enough time with me lately."

TBC


	8. Chapter 8

**NOTE: **Now that I've figured out how to post, the internet connection at work went hinky yesterday and this morning. Sometimes I think computers hate me. Anyway, sorry for the delay, yet again.

The Return Part 2: Favorite Son - Chapter 8

John smiled as he walked toward the mess hall to meet his team for supper. He felt good, for the first time in at least four days, and he was pretty happy about it. The headache had finally disappeared while he'd slept and he didn't feel like he'd spent hours running with Ronon. He wasn't exactly a bundle of energy, but the lethargic, too heavy to do anything feeling had finally dissipated.

Entering the large room, he immediately spied his friends, some already seated, but others just arriving with their food. Moving to the food line, he quickly garnered a tray and joined his team at the table, taking the open seat at the end.

"Hey guys, how'd it go today?" John asked as he arranged his plate and drink.

"Good," replied Elizabeth as she studied him. "You look like you feel better."

John smiled and nodded. "I do actually. Headache free all day and I can't complain."

"Definitely an improvement over that corpse look you had going on earlier. You could have been in a zombie movie and they wouldn't have needed make-up," said Rodney as he chewed a bite.

John was in too good a mood to get angry and besides, he'd seen his reflection a few times and knew Rodney wasn't far from the truth. "Well, I'm glad you approve," he said lightly. After waking to his team assembled in his room, he'd slept most of the first two days, waking a few times to eat soup they'd brought or get checked by Carson. He'd managed to stay awake several hours yesterday, but the headache had still been pretty bad, so he'd barely gotten out of bed. He'd been surprised to wake this morning with no headache and feeling pretty good.

"What did you do today, Colonel?" asked Carson.

John chuckled. "Subtle, Doc. I read some things Helia gave me about Atlantis and some of the mission reports from the Ancients who used to live here. I talked to Savill about security and their version of gate protocol and our possible use of jumpers. After lunch I had a nice, huge nap."

"Good boy," Carson said approvingly.

"I can be good when I want to be," said John.

"Aye, I know. That's what makes the other times so annoying."

"Mmm, hadn't thought of that." John realized a little late that he'd just dug himself a nice hole.

"So, what did they say about using the jumpers?" asked Rodney.

"Well, they said I obviously knew how to fly them from our entrance, but Helia still wants me to go up with one of their pilots to make sure. Once their guy clears me, then we just go through regular channels to use one, kind of like we did with Elizabeth. Sounded very reasonable." John was obviously pleased. "Rodney, what'd you do?"

"I got my new lab set up yesterday and met with the two scientists that will be working under me. They aren't all that smart, as near as I can tell, but they are eager, so I guess that's something. They do know some things about the Ancient systems that I'm not familiar with, so I suppose they'll be helpful in that area. My first project is to find out why interacting with the city from the chair is wiping you out so much right now."

"Any progress on that?" asked Elizabeth.

Rodney nodded and waved his fork once. "Yes, actually, but I'm not done yet. I think the damage coupled with something the Asurans did is combining to drain the power and make the chair draw some from Sheppard, but I can't figure out how it's doing that. I think I'll have it in one or two more days though, at least by the time Carson clears him."

John turned to Carson. "When might that be, by the way? I feel really good today."

"Aye, I know, but you can't rush it. This is the first day you've been out of bed for more than a few minutes and the first day you've felt like leaving your quarters. You need a few more days to build your strength. I'd like to do another scan tonight, since you do feel so much better and compare it to the one we did four days ago."

John groaned and rolled his eyes. "I hope there's no radiation involved in these scans, as much as you run them on me."

"Why, planning on making some little Sheppards?" asked Rodney impishly.

"Maybe, maybe not. But I'd at least like the option."

"No radiation, Colonel," said Carson as he grinned. "And if you can stay out of trouble, I'll cut down on the scans."

"Agreed," said John. "You still working with Emira?"

"Yes, and she's amazing. She's been showing me how to work all the Ancient equipment and it's just wonderful. I wish I had known about some of it when the expedition was here. We could have used it a few times."

"What about the rest of you guys?" asked John.

Elizabeth nodded toward Ronon and Teyla. "The three of us met with Helia and Savill about future missions. They went over mission protocol and we explained our system. I pulled some of the mission reports from our time here and we talked about them, evaluated the things we did right and wrong and how they would have done them differently. I think they were trying to get a feel for how well we knew what we were doing."

John looked from Elizabeth to Ronon and then Teyal. "So, did we pass?"

Teyla smiled and nodded. "I believe that we did. They made a few suggestions, but they also admitted once or twice that the way they would have handled the situation would probably not have worked as well as what we did. I think they were satisfied with our skills."

"I do too," added Elizabeth. "We even have a mission picked out for when you're cleared. Something easy to start with."

John sat up straighter, raising his brows. "Oh, like what?" He was trying to school his voice so they didn't hear the annoyance and touch of hurt that they had planned out a mission without him. He hadn't expected them to wait on him to set things up, but he hadn't expected them to plan missions either.

Teyla, apparently sensing his unease, leaned forward to put her hand on his. "It is simply a visit to check on the people of M3P-774 to see if they are still interested in trading the baccarupia root for help in irrigating their fields."

"Oh, okay . . . that's not much." John wasn't sure if he was relieved they hadn't planned a real mission without him or disappointed that their first mission for the Ancients was to be so lame.

Teyla, Ronon, and Elizabeth laughed, making John self-conscious. "What?"

"Dr. Weir knows you well," said Ronon between chuckles.

John frowned and sat back in his chair. "What do you mean?"

Elizabeth shrugged her shoulder. "Helia wanted us to plan the first mission, but we were a bit uncomfortable doing it without you. I knew you'd feel like we'd gone over your head or behind your back or something, and realistically, if you're going to lead the mission, you should be there to help plan it. So I suggested we do something simple and boring so you wouldn't be so . . . "

"Pouty? Sulky?" offered Rodney.

Ronon was still wearing a broad grin. "She said if we planned a good, exciting mission, you'd be pissed you didn't get any say-so in it, but if we planned an easy mission, you'd be annoyed it was so boring."

"We call that damned if you do and damned if you don't," offered Rodney.

"Stop helping," John said to the scientist. "Anyway, I'm not pissed or complaining. All I said was _oh_. That doesn't mean anything."

"Nice try," said Rodney.

John kicked Rodney under the table, causing the man to yelp. "You're ruining my good mood, so shut up."

Rodney grunted, bent over sideways in his chair so he could rub his shin. "I think I liked you better when you slept all the time. It was less painful."

oOo

John lay on the exam table, watching the scanner move to the end of the bed and stop. Carson and Emira stood talking and pointing to the screen of the Ancient device for several minutes while the pilot's patience slowly dissipated. He finally pushed himself up to his elbows. "Okay, what's the verdict? Am I cleared for duty or not?"

John would be the first to admit he was antsy. He'd been good for several days now, pointedly not exercising, eating regularly, and lying down in the afternoon, even days when he couldn't sleep. He'd done everything he was supposed to and was sick of it. If they didn't release him from their care, he was pretty sure he would have to do physical damage to someone.

Carson and Emira smiled at each other and moved away from the foot of the bed. Emira patted him on the lower leg. "Congratulations, Colonel. Carson can take care of things while I go see about test results for another patient."

John watched her leave and then looked up at Carson, his eyes wide. "Does this mean I'm done?"

Carson nodded. "Aye, this latest scan shows everything back to normal and you're energy levels have been good the last couple of days."

John immediately sat up and swung his legs over the side of the table. "That's great news, Doc. Thanks."

Carson gripped John firmly by the wrist before he could hop off the bed. "Colonel, wait a minute. We are releasing you to active duty, but you are not to go near that chair. There's something wrong there for it to be affecting you as it is and until someone fixes it, you are not to sit in it again."

John's expression clouded slightly, but he nodded. "Okay, I won't. Rodney's been working on something to fix it."

"That's fine, but I clear it before you try anything. Promise me."

John frowned slightly. "Okay," he drawled. "You're making this seem serious, Doc. It gave me a headache and made me tired, but it's not that big of a deal."

Carson's expression was serious as his eyes drilled into those of the Colonel. "Yes, it is a big deal. You have no idea how erratic your readings were for a while. And we didn't even scan you until the day after the event. I shudder to think how bad it probably was right after you sat in the chair. We don't know what kind of long term effects multiple exposures to that kind of disruption can cause, but I'm guessing increased chances of stroke and seizures, as well as possible brain damage. This is nothing to make light of."

John nodded as he slipped off the table and gripped Carson's arm. "Okay, I'm taking it seriously and I will stay out of any and all Ancient chairs until you have officially approved." His tone was serious, not mocking and he looked the doctor in the eyes as he spoke. He wanted Carson to know he wasn't blowing off his concern or instructions.

Carson let out a deep breath and relaxed. "Okay, thank you Colonel."

John grinned. "I'll be fine, Doc. Really. Be sure to let Helia and Elizabeth know I'm free because they probably won't believe me."

Carson watched Sheppard as he walked off. "I'll be sure and warn them."

oOo

Renato watched the scientist from Earth, almost gritting his teeth in anger as the man berated his colleagues as if they were stupid. It wasn't like he hadn't done the same thing on numerous occasions, but they were a master race and this man was merely a human. His arrogance and pride made Renato's blood boil, especially when he talked to him as if he were talking to a child. He had no idea what had possessed Captain Helia to give this simple being lab space, much less to give him Renato's station just because he had previously worked there.

"Hey, McKay!"

Renato tore his glare from Dr. McKay to see a tall, dark haired man enter. He looked familiar, one of the Earth people he remembered.

Dr. McKay rolled his eyes as if he hadn't wanted to see the man. "What is it Colonel? Some of us are busy working."

"I am officially released from medical leave and am back on active duty, as of fifteen minutes ago." The tall, slender man grinned proudly.

Renato slid slowly down to the end of his workbench so he could eavesdrop on the conversation. He kept his head mostly down so as not to appear to be listening.

"Well, bravo for you, Sheppard. If you're having an urge to blow something up, I'd appreciate it if you do it elsewhere." McKay was looking at something on his computer screen and not even looking at the man he was talking to. Renato decided that was just another side of his multi-faceted rude behavior and he was curious to see how the other man would react.

Sheppard sat down on a stool beside McKay and peered across his arm at the screen. "What are you working on, the chair problem? Find anything yet?"

McKay paused and looked at the man. "Yes, that's what I'm working on and quit hanging over me. You know that drives me crazy. I've been running simulations and, boy, could I use Radek about now. Never thought I'd miss that crazy Czech, but I do now."

Sheppard grinned and leaned back a bit. "You knew you'd miss him, you guys were friends, no matter how much you tried to pretend differently. It would be kind of cool if he was around again. Maybe we could talk to Helia about him coming back pretty soon."

Retanto had to suppress the urge to throw something. Another scientist from Earth in his lab was not what he needed or wanted. He'd have to try and squash that idea before it ever got off the ground.

"That's it!" said McKay excitedly, jumping up off the stool he'd been perched on. "I think I have it figured out."

Sheppard seemed excited as well, slapping McKay on the back. "Great! I knew you could do it. Now let's go explain it to Carson so he'll let me sit in the chair again."

That's who the tall man was, the Earth man who had the special link with Atlantis. The name Sheppard now seemed familiar and he was sure this was who they had been talking about. Another example of a human trying to be more than his station allowed.

"Just hold on gene boy, I won't be ready to run this program until tomorrow at the earliest. It still needs some tweaking."

Sheppard bristled. "I told you not to call me that. Let's go ahead and explain it to him so he can have time to panic and get over it. That way, by the time you actually have things fixed, he'll be willing to let me try it."

McKay seemed to consider this before nodding. "Okay, but we tell Elizabeth and Helia at the same time so I don't have to go through this long explanation three times."

"Short."

McKay frowned and tilted his head forward just a little. "What?"

Sheppard grinned again, his smile uneven. "Keep it short, McKay or they'll never approve it."

"Yes, yes, well, I suppose it's best considering none of you would get the long version anyway."

Renato gripped the instrument he was holding tightly, seething again at the ego of the man. Someone needed to take that man down a step or two and he figured he might just be the one to do it. He smiled as he watched the two men leave the room.

oOo

John paced back and forth outside the conference room, periodically stopping to study the corridor.

"John, come in here and sit down," said Elizabeth, frowning at him as she stood in the doorway.

John sighed and nodded, moving toward the room as ordered. He was about to cross the threshold when movement in his peripheral vision caught his eye. Carson and Emira had just rounded the corner and were headed for the room. "It's about time," he muttered as he followed Elizabeth into the room and took a seat between her and Rodney. "They're finally coming," he said to the scientist.

Rodney looked at his watch and then up at the two physicians just entering the room. "Nice of you to join us, doctors."

Carson threw Rodney a glare. "We were tending to patients, Rodney. That is our job, after all."

Helia, sitting at the head of the table, waited until the doctors had taken a seat to begin. "Dr. McKay, I understand you have some news about the problems Colonel Sheppard had with the chair."

Rodney nodded and looked up from his computer screen. "Yes, I do. I think I have identified the problem and developed a solution. The Asurans loaded a program of their own onto the chair controls, one which I only recently discovered."

The sound of someone clearing their voice drew everyone's attention to Dolon, who was looking purposefully at Rodney.

Rodney sighed and nodded. "Okay, so Dolon and I discovered the program. Anyway, it seems to have been meant to keep Ancients from activating the chair, but Sheppard was able to somehow override it. The original program kept the chair from drawing power from the ZPM, but Sheppard or Atlantis or maybe both working together just rerouted the power, using the Colonel as a kind of adapter. That's why it had the effect it did."

Carson looked at Emira and then back to Rodney. "Did you say you could fix it?"

Rodney nodded. "Of course, remember who you're talking to here. I have a program put together that should shut the Asurans' little addition down. I just need to tweak it and we'll be ready to go."

"And you're sure it will work?" asked Elizabeth.

"Yes, reasonably sure. It should work . . . I mean, there's no way to know for sure until we try it, but it should work." Rodney glanced around the room, his gaze drawn to Sheppard and the storm cloud expression on his face. "Uh, it will work."

Carson looked at Emira again and they talked softly for a moment before he turned back to the group. "You don't sound very certain and I surely don't want the Colonel to be exposed to that again."

"We could start out with a link for just a few minutes to try it," suggested John.

Rodney looked relieved at the rescue attempt. "Yes, we could just shut it down after a few minutes and then see how Sheppard feels. And I would be monitoring, so I'm sure I could tell if it was working, now that I know what to look for."

Carson and Emira whispered another few minutes. Carson nodded and faced the waiting group. "I want to check the Colonel before you try it and we want to be there with monitoring equipment during the trial. I want to be handy in case anything goes amiss."

"What kind of monitoring equipment?" asked John, frowning and narrowing his eyes.

"Cardiac, EEG, and blood pressure," replied Emira.

John shook his head. "No, no, no, I don't need all that. How am I supposed to concentrate with all that gear on me?"

Carson grinned, making John think of the cat that swallowed the canary. "But you don't have to concentrate like the rest of us. You should manage fine. Besides, we will not approve of this otherwise.

John was at a loss, unable to refute Carson's argument, but certainly not wanting to comply. "Elizabeth?"

Elizabeth smiled and for once was happy to announce, "It's not my call." She looked at Helia, as did everyone else.

Helia looked at the people surrounding the table for a moment before making her decision. "Colonel, I do not think it an unreasonable request and we all want you to be safe. Dr. McKay, Dolon, when you are ready to proceed, let me know. Dr. Beckett and Emira will monitor Colonel Sheppard while he connects with Atlantis. When everyone is satisfied that the problem has been repaired and Colonel Sheppard is no longer in danger, the monitoring will no longer be required."

"Thank you," said Carson. "Look at this way, Colonel. We had talked about doing this anyway as part of our study. Now you can get it done and out of the way."

"Fine," said John, looking anything but pleased. "Rodney, can we go tomorrow?"

Rodney looked down at his computer screen and pecked on the keys a few seconds. When he stopped, he sat staring at the screen again and nodding. "Tomorrow should be good, probably about mid-morning. I'll finish tweaking the program today and Dolon and I can set up in the morning first thing. We'll call everyone when we're ready."

Carson looked at John. "Colonel, I expect to see you after breakfast for a once over before we begin."

"I figured that," said John. "So, if Rodney has this thing fixed, can I use the chair when I need to, because Atlantis and I still have a lot of stuff to fix." He looked over at Helia. "With your permission, of course."

Helia nodded. "We would be grateful for the help as long as it goes through me first."

"We'll see how it goes tomorrow," said Carson. "I don't like to make promises I later discover I can't keep."

John let out a slow breath and nodded. "Fair enough."

oOo

John spun the stick in his right hand around slowly before gripping it again. He shifted his feet, moving sideways in a wide circle and facing Teyla as she did the same.

"You are certain you are allowed to do this," said Teyla, never taking her eyes off her opponent.

"Beckett said full duty, that means everything. I specifically asked about running and he okayed that, so I know this is okay."

"Good," she replied evenly. "It has been a long time. Perhaps I should take it easy on you."

John saw Ronon enter the room through the door to his left. His attention momentarily distracted, Teyla seized the opportunity and moved. He turned quickly to fend off her attack, but he'd been caught off guard and it didn't take long for her to knock the stick from his right hand with a painful smack across the knuckles. The next thing he knew, he was on his knees with Teyla's stick across his throat as she stood behind him. The position was all too familiar.

Teyla eased her stance and released him, stepping back so he could stand. John rubbed his throat as he got to his feet. He glanced over at Ronon, who stood leaning against the wall and grinning. "Thanks, buddy."

"You can't get distracted, Sheppard. That could get you killed."

"So I noticed," he said dryly. John glanced back at Teyla. "Nice move, as always."

Teyla bowed her head slightly. "Thank you. I know you have not been able to practice for a while."

John nodded as he and Teyla took up their ready stance. "I didn't have anyone to practice with on Earth, so I'm really rusty."

"Then I am even more happy to have you back as a sparring partner. We will slow down until you have had sufficient time to retrain yourself and remember the moves."

"No, that's okay," said John as they began to circle one another. "I'll get back into the swing of things faster if you don't take it easy on me."

Teyla gave a sly smile. "As you wish." Two minutes later, John was flat on his back with her stick at his throat again.

Ronon's laugh rumbled from across the room. "Be sure you leave enough of him to sit in the chair tomorrow or McKay will be furious."

John couldn't help but think of their conversation a few days ago about crushing his ego. Maybe he should have let her take it easy on him. His aching back and neck were telling him that would have been the smart thing to do.

TBC


	9. Chapter 9

The Return Part 2: Favorite Son - Chapter 9

John hurried down the hall, knowing Rodney was probably about to blow a gasket. A voice suddenly yelled in his ear, confirming his prediction. "Sheppard, where are you? We're all sitting here wasting time while you lollygag around half the day."

John sighed, not sure whether to thank Helia for the radios or curse her. She had finally trusted them enough to let them use communication devices so they could keep in touch when they were scattered across the city.

"I'm coming, Rodney, keep your pants on. Beckett wanted to do his infamous one-more-scan thing. I'm almost there."

"Well, I hope. You're the reason for this fiasco and you're late for the party."

John nodded as he stepped past Ronon and Teyla, parked in the corridor to be both near and out of the way, and through the door to the chair room. "Okay, I'm here," he announced.

"Finally." Rodney stood from his position beside the pedestal and leaned over, as if looking around Sheppard. "Where's Carson? He said if we started without him he'd skin my hide with his rustiest scalpel."

John looked at Rodney blankly. "Carson has rusty scalpels?"

Elizabeth grinned and exchanged a strange look with Helia, making John a little self conscious at the normally natural banter. He ignored Rodney's little monolog on the dangers of angering Carson as he took the opportunity to look around the room. Dolon was there, managing the console against the far wall and looking bored. Helia and Elizabeth stood to one side, no doubt just trying to stay out of the way. Rodney had his computer hooked up to the pedestal of the chair. John looked longingly at the chair and realized he missed Atlantis. He was always in contact with her to a certain degree, but since returning, he felt a deeper connection and seemed to almost crave the link that came with the chair. He likened it to the difference between talking to a close friend or relative over the phone as compared to actually getting to visit them.

"Colonel!"

John jerked slightly, shifting his eyes to Rodney, who had somehow moved to stand right in front of him. "What?"

Rodney eyed him suspiciously. "You okay? You kind of zoned out there for a minute."

John smiled sheepishly. "Yeah, sorry. I was just thinking about something."

Carson and Emira entered the room, with Carson carrying a small bag. Rodney looked relieved and stepped back toward his computer. "Well, it's about time. I guess doctors are even slower than flyboys. Can we start now?"

Carson set the bag on a table and began opening it. "Hold your horses and let us get the Colonel connected to the monitors." Carson pulled something out of the bag and handed it to Emira, who then walked over toward John.

"Colonel Sheppard, would you sit down please?" she asked.

John took his seat in the chair, but did not lean back or activate it yet. Emira removed the radio and set it aside before attaching a small metal disk to each of the Colonel's temples. She then lifted his shirt and attached two more disks to his chest. As she finished, Carson handed her a square object similar to a datapad. It had a screen covering the top three quarters of the device and two rows of oval keys with Ancient symbols across the bottom. Emira touched two of them and then removed what looked like a pen on a cord from its groove. She touched it to one of the disks on John's temple and then the other. After touching two more symbols on the pad, she then lifted his shirt once again and touched the pen to the two disks on his chest. Lowering his shirt, she ran through a sequence of several symbols before smiling at John.

"All right, we're ready."

John's jaw dropped a bit. "That's it?" He'd been expecting a crowded room full of monitors and their connecting wires, distracting and annoying him.

Carson smiled smugly. "Aye, Colonel. We're using a portable monitoring system developed by the Ancients."

Rodney had been watching, clearly fascinated. "It's wireless and everything. That's great, Carson. Maybe you should just have Colonel Calamity wear that all the time. You could monitor him from the infirmary and know instantly when he's gotten into his next life-threatening mess."

John shot Rodney a withering look before turning back to the physicians. "If I'd known it was this easy, I would never have complained."

"It's designed for short term field use, so you have to be close to the patient for it to work and it won't work for long periods, thus making it impractical for Rodney's suggestion, but it's perfect for this. Emira showed it to me this morning."

"I have to admit, it's pretty cool. So, are we ready?" asked John.

"Aye, you're ready as far we we're concerned." The two doctors stepped back a few feet, watching the screen in Emira's hands. "We're getting clear readings on all systems."

Rodney went back to his station, sitting in the chair he'd pulled up to where he had the computer plugged in. "Dolon?"

"I'm ready here," replied the Ancient, sounding almost as bored as he looked.

Rodney nodded as he hit a key on the laptop. "Okay, Colonel, go when you're ready."

John leaned back in the chair, feeling the link to Atlantis slide into place like a well-fitted glove. Almost instantly, he was with her and she with him. They communicated without words and almost without thoughts. There was a welcoming embrace, a greeting reserved for no other. And then he was lost in her as she showed him another side of Atlantis. He took in areas that needed repairs as well as places he'd never known were there. He could feel the energy ebb and flow as different areas of the city drew power from her core.

"Colonel? I need you to come back to us."

"Just a minute," he mumbled, trying to keep the connection in place. He wasn't ready to leave her warm embrace.

"No, Colonel, now." Carson and he was being firm.

John let the connection go, making him suddenly feel cold and alone. He opened his eyes to find Carson staring down at him. "Doc."

Carson seemed a bit relieved. "Colonel, you had me worried."

John sat up straighter in the chair. "I'm fine, I just . . . we were connected." John looked down uncomfortably.

"How do you feel? Headache?"

John relaxed a bit as he looked up at the doctor. "Actually, no. I'm a little tired, but nothing like before. How long has it been?"

Emira looked up from the screen of the monitor. "About twenty minutes, Colonel."

John was amazed. It seemed like barely a few moments to him. He ran one hand through his hair, feeling somewhat disoriented at the change.

Carson looked across Emira's arm to the screen and nodded before turning back to John. "Okay, let's get you to the infirmary for a full scan and I'd like to monitor your EEG readings for a while."

John frowned, wanting everyone to go away and let him go back to Atlantis. "Look, I'm okay Carson. Atlantis was just showing me some things and I need to get back. I'll come down for the scan later."

Carson crossed his arms, his tone stern. "No, you'll come down now. We've got contradicting readings on your EEG and we need to study it now while it's still fresh so we can watch how it returns to normal, or at least normal for you. Atlantis will still be here tomorrow."

"What was Atlantis showing you?" asked Helia as she and Elizabeth moved closer.

"The city, in a way I've never seen it before. There are several damaged areas I can help repair from here."

"Well, as Carson said, it will still be there tomorrow and your health is important. Go with Carson and do as he says," said Elizabeth.

John looked to Helia, almost wishing she'd override Elizabeth. And the Ancient looked like she wanted to do just that, but in the end she didn't. She finally just sighed and looked squarely at John. "Colonel Sheppard, you need to do as the doctors say and accompany them to the infirmary please."

John nodded, realizing he was outnumbered and not winning this battle. Carson helped him stand, but he pulled away from the physician's grip as soon as he was on his feet. "I can walk. Contrary to popular belief, I'm not an invalid." He marched past Carson and out the door, swooshing past Teyla and Ronon without a word.

"I'd say he's not happy," commented Ronon. "Can't blame him though."

"They are just trying to keep the Colonel from being harmed," said Teyla.

They watched as Carson rushed out of the room, trying to catch up to Sheppard. Emira stepped out a moment later, only to be called back by Helia. Neither woman saw Teyla and Ronon standing in a small alcove a few feet away.

"Emira, I need to talk to you a minute."

Emira stopped and looked back at Helia, hesitating before she stepped back to stand next to her captain. "Yes, ma'am?"

"I want you to let me know what you find. Make some excuse to come to my office as soon as you know anything about Colonel Sheppard and the connection to Atlantis."

Emira paused, obviously struggling. "Captain Helia, I don't mean to sound disrespectful, but Carson and I will be making a full report on everything we find to both you and Dr. Weir. Can't it wait until then?"

"No, I want some time to think before that happens. Look, I'm not asking you to hide anything or lie about your results, I just need some prior warning about what the results are going to be."

Emira frowned, but finally nodded. "All right, I'll come as soon as we run the scan and examine the results." The doctor turned and hurried down the hall while Helia went back in the chair room.

Ronon looked down at Teyla, his jaw clenched in anger. "It seems we're the ones who should not have trusted _them_."

Teyla nodded. "I knew she seemed abnormally interested in the Colonel's connection to Atlantis. We need to talk to Elizabeth."

Ronon nodded. "I agree. We'll tell her what we heard as soon as we can get her away from Helia."

oOo

John sat up and swung his legs over the side of the table. "So, are we done?"

Carson walked up to the Colonel as he entered information on the data pad in his hand. "Does this mean you're speaking to me?"

John sighed and rubbed the back of his neck. "I was never not speaking to you, I was just aggravated. So am I alright or what?"

Carson lowered the pad and looked at his patient. "Everything looks fine but the EEG. I'd like to hook you up to the monitor for a while."

John moaned. "What's wrong with it and how long are you talking about?"

"You're showing . . . let's just say that according to your EEG, you're in a coma while being fully conscious, or at least that's what registered while you were connected to Atlantis. It's almost back to normal now, but there are still some odd fluctuations. I'm just guessing on the time, but I'd say an hour or two at most."

John sighed and nodded. "All right. I did say that you and Emira could run some studies, just make sure this counts as one."

Carson chuckled. "Aye, I believe that it does."

"Where do you want me?" he asked as he slid off the table. Carson led him to a bed in the back corner with several monitors around the bed. "Ready for a disaster, Doc?"

"Just getting prepared for you, Colonel."

John grunted. "I could take offense to that."

"I was just thinking about your history when I set things up. Now, sit on the bed and I'll get you hooked up. The Ancient version has less electrodes, so it will only take a moment."

John settled on the edge of the bed as Carson attached electrodes to his temples and forehead. "Where'd Emira disappear to?"

"She said something about needing to see Helia. I told her I could finish here." Carson finished attaching electrodes behind John's ears. "All right, that's it. Let's get you lying down." He helped John lie back against the pillows and then turned on the machine. Watching the screen for several moments, he finally nodded. "Looks like everything is working okay. I've got some things to attend to, so you just lie still. I'll check on you in a bit."

John watched Carson walk away and realized he once again was lying around with nothing to do. How had his life become so boring?

oOo

Elizabeth waited until the door to her quarters closed before speaking. Once she knew they were alone, she faced Ronon and Teyla, both with strained expressions on their faces. "Okay, tell me what's going on."

Teyla repeated the conversation they had overheard between Helia and Emira. "I do not believe Emira felt the actions were appropriate."

Elizabeth nodded. "It sounds like she's just following orders. And Helia hasn't actually asked her to do anything specifically hurtful or wrong, but once again, it looks like she doesn't trust us."

"Or is planning something we wouldn't like," said Ronon. "I say let's get Sheppard and go. I'm tired of the sneaking and backstabbing."

Elizabeth nodded. "I'm tired of it as well. I would like to hear what Helia has to say first. When Carson and Emira have all their information sorted, they'll be calling a meeting to discuss the results. I think we need to confront her then and possibly take our leave."

"We should tell the others before the meeting," said Teyla.

Elizabeth put one finger to her chin, tapping it several times. "Okay, why don't the two of you find Rodney and I'll see if I can get into the infirmary and talk to John and Carson without an audience."

"Agreed," said Teyla, with Ronon nodding his acceptance.

oOo

Emira stepped into Helia's office. "Captain Helia, I have come as you asked."

Helia looked up from her desk and stood, indicating one of the chairs. "Thank you, Emira, what can you tell me?"

Emira ignored the chairs, choosing instead to stand. "I've only been able to do a preliminary scan of the test results, so I can't tell you anything definite. I do know that Colonel Sheppard shows brain waves comparable to someone in deep coma at the same time as waves like someone who is conscious when he is connected to Atlantis. It is very . . . unique. There is also a small periodic pattern that is different than any I've ever seen. I also noticed that an area of Colonel Sheppard's DNA is activated during his link with the chair."

"Is that what Dr. Beckett refers to as the ATA gene?" asked Helia.

"No, although that area is active as well. This is a previously unidentified area and it did not activate until Colonel Sheppard connected to the city. I have not had time to check the database to compare it to our DNA standards."

Helia nodded. "All right, see what you can find out. Is Dr. Beckett aware of this?"

"He didn't mention it. I'm not sure if he fully understands the way the monitoring equipment works, so it is possible he missed it."

Helia looked slightly relieved. "Okay, do not call his attention to it for now. Study it to see what you can find out and then report to me."

Emira shifted her weight back and forth nervously. "Captain, Carson and I are supposed to be working together on this. We can solve the problem faster if we share information and work together."

"Maybe later, Emira. Do as I tell you."

"Yes, ma'am," said Emira, turning and walking and slowly from the office.

Helia knew Emira was not happy with her orders, but she didn't understand what was at stake. Helia would make her see the benefit of keeping certain secrets later on.

oOo

Rodney walked quickly into the lab and set up his computer at his station. Dolon was right on his heels.

"Can we load the information into the main system from here?" asked Dolon.

"Yes, I've been doing it for almost three years now. I had to do a little creative connecting, especially after you guys or the Asurans disconnected my little set-up, but I have it all put together again." Rodney immediately began connecting his laptop to the Ancient system.

"That's actually quite clever. I noticed you have created some programs to mesh with the chair systems and download information directly to your computer."

Rodney smiled, proud to have an Ancient that not only understood his work, but appreciated it as well. He was beginning to like this guy. "Yes, well, we had to. We were trying to . . . hello, what's this?" Rodney noticed the Ancient panel he had connected his computer to had a blinking light, something he'd never seen before.

Dolon looked around the opened computer lid to see the light. "Dr. McKay!" he yelled as he grabbed the scientist's arm. Just as he started to pull Rodney back, the terminal exploded in a flash of sparks.

TBC


	10. Chapter 10

The Return Part 2: Favorite Son - Chapter 10

Ronon and Teyla walked into the lab just in time to see Rodney and Dolon thrown back and hear the small explosion. Flames and sparks flew out toward the two men as they yelled and hit the ground. The right arm and shoulder of Rodney's shirt was on fire and Ronon grabbed a jacket from a chair and immediately began smothering it while Teyla radioed Beckett for help.

Rodney rolled around on the floor moaning as Dolon struggled to sit up. "What did you do to him?" yelled Ronon, standing tensed and threatening over the man.

Teyla came to kneel beside Rodney. "Ronon, calm down. I believe he was trying to pull Rodney away. Rodney, tell me where you are injured."

Rodney moaned loudly, his hands on his face. "My face is burned. Oh my God, I'm probably blind. Am I on fire? I smell something burning, is it me?"

Teyla put a calming hand on his left shoulder. "Rodney, you need to lie still. Ronon had extinguished the fire. Just keep your eyes closed and relax. Dr. Beckett is on his way."

"Easy for you to say, you aren't the one who got blown up," cried Rodney, his voice high pitched and panicked.

Teyla continued to lightly grasp his good shoulder, trying to comfort and calm the scientist. "I do not believe you are seriously injured, thanks to Dolon." She turned to the Ancient, sitting slumped beside her and rubbing the back of his head. "Are you injured?"

Dolon grimaced, apparently hitting a sore spot. "Just a few bruises, I believe. Dr. McKay took the brunt of the force."

Rodney lowered his hands, his breathing having evened out. "Thank you . . . for trying to pull me away. If you hadn't . . . I might be dead."

Dolon simply gave a small nod. "You are welcome. I do not understand how this could have happened unless . . . "

"Unless what?" asked Ronon, narrowing his eyes at the scientist sitting on the floor.

Dolon looked from Ronon to Teyla, obviously troubled. "I'm afraid this may have been an attack on Dr. McKay. I do not see how the station could have overloaded on its own. I assure you, a full investigation will be done."

Teyla's mouth hung open in shock. "But . . . I do not understand. Who would do such a thing? Why would someone wish to harm Rodney?"

Rodney winced. "Oh, I can think of a likely candidate."

Dolon nodded and sighed. "As can I. Whoever it was, they have shamed us all."

oOo

"Carson, how much longer?" whined John, looking up at the physician as he checked the monitor.

Carson smiled. "You really should work on your patience, lad."

John sighed. "So you keep telling me." A flash of pain through John's head led him to sit up so suddenly that he almost pulled the electrodes loose.

Carson moved quickly to his side. "Colonel, what's wrong?"

John rubbed his forehead a second and then let his hand drop. "Rodney . . . something's happened to Rodney."

Carson was about to ask him what when his radio came to life. John watched as he tilted his head, listening, before nodding and responding.

"All right, love, keep him calm and we'll be there in a minute." Carson returned his gaze to the worried face of Sheppard. "That was Teyla. There's been a small explosion in the lab and Rodney is injured."

John reached up to begin pulling off the pads connected to his head, but his arm was stopped midway by Carson. "Colonel, you need to lie back down. I'll handle this."

John shook his head. "Rodney's hurt, I'm coming with you."

"There is nothing you can do and you'll just be in the way. I'll be bringing him back here and you'll have a front row seat to keep an eye on him. I need you to stay put and stop slowing me down."

John hated that Carson was right. He couldn't help and he probably would be in the way. "All right, I get it. Go!" When Carson accepted his word and let go, John forced himself to lie back against the pillow. He watched as Emira raced out of her office to join Carson, having obviously received word about the explosion from her people. They assembled a med team and raced out of the infirmary with two gurneys and several nurses. John focused on not jumping out and following them.

Fifteen minutes later, John propped himself up on his elbows when he heard people approaching the infirmary. He watched as a gurney clattered by with Rodney. The injured man held his right hand, wrapped in white bandages, suspended just above his chest.. A white cloth lay across the upper part of his face, but John could see red, burned skin peaking out around the edges. He swallowed hard when he realized Rodney's eyes were covered and hoped they weren't damaged. He was so focused on watching the flurry of activity around his friend, he almost didn't notice Ronon and Teyla come up to stand beside him.

"Dr. Beckett says that Rodney will be fine," said Teyla, reading the fear in his face.

"What about his eyes?"

Teyla smiled briefly. "He must check more thoroughly, but it seems Rodney closed his eyes before the blast and it is mostly burns to his skin and eyelids."

"He has no eyebrows," said Ronon, his voice a deadpan.

John blinked and stared at the man. "No eyebrows?"

"Singed them right off," said the ex-runner, his expression blank.

John felt himself relax a little, a small smile twitching at the corners of his mouth. "That could be . . . interesting."

Teyla looked sternly from Ronon to John. "His eyebrows are not completely gone and I do not feel it would be appropriate of either of you to make fun of him."

John frowned slightly, the smile disappearing. "Teyla, I'm hurt. Why would you even suggest such a thing?"

Teyla grimaced and shook her head. "Why indeed," she muttered.

John had to admit, he felt a little better. He was still worried about Rodney, burns could be very painful and Rodney's pain threshold was notoriously low. But he was relieved that there would apparently be no lasting damage or long, drawn out recovery. It could have been much worse. And when the scientist felt better and they were sure he would be okay, he could tease him relentlessly about his lack of eyebrows. John let a small smile creep across his face as he reached up to scratch at the electrode stuck to his right temple.

Teyla slapped his hand, knocking it away. "You should not do that," she admonished.

"It itches," John complained. His attention was diverted from the discomfort of the electrodes to the door as Elizabeth rushed through the opening. Seeing Teyla and Ronon at John's bedside, she made her way over while scanning the rest of the infirmary for Rodney. Her eyes focused on the flurry of activity around the injured scientist

"What happened and how is Rodney?" she asked as she stopped beside Teyla.

Teyla followed her line of sight. "There was an explosion in the lab at Rodney's station. Dolon realized something was wrong and was able to pull Rodney far enough away to prevent serious injury. He has some burns, but Dr. Beckett did not feel they were serious."

John widened his vision enough to realize for the first time that Dolon sat on another gurney a few feet from Rodney. A nurse was treating him for burns on his arm. One side of his face was reddened, but not as badly as Rodney's had seemed. And at least he had eyebrows. "Is Dolon okay?"

Teyla nodded. "Yes, I believe so. He only had some minor burns."

"Do they know what caused the explosion?" asked Elizabeth.

Ronon grunted. "Dolon says he's pretty sure it had to have been set up to explode when McKay connected his computer to the Ancient systems."

"Someone tried to kill Rodney?" asked John incredulously.

"Dolon was unsure if the intent was to kill or merely incapacitate Rodney," said Teyla.

John sat up and reached up to pull the electrodes off. "Enough of this. I need to talk to Helia."

Elizabeth placed a restraining hand on John's arm. "Wait. There's something you need to know. I was on my way to talk to you and Carson when I heard Teyla call for a medical team." Elizabeth crossed her arms, looking uncomfortable. "Teyla, tell John what you and Ronon overheard."

Teyla nodded and quietly relayed the events to John, with Ronon giving a nod occasionally. John seethed with anger and feelings of betrayal. He was thankful Carson wasn't monitoring his vital signs, because he was pretty sure his blood pressure would be off the scale. He had a deep urge to hit something that resulted in him clenching his fists tightly by his side. He couldn't help but notice that Ronon looked almost as angry as he felt.

"Stay here with Rodney. I need to go find . . . " He trailed off as Helia walked into the infirmary. She looked around and saw Dolon and then John and his team. Giving them a small nod, oblivious to their anger or knowledge of her actions, she walked over to stand beside the injured scientist. John slid off the bed and marched over to join the two Ancients.

"Helia, I need to speak to you." He knew he did a poor job of keeping the anger from his voice, but he didn't care. After he told her what he wanted to say, there would be no doubt about his feelings.

Helia looked uneasy. "Of course, Colonel, but perhaps later. I need to get a report from Dolon about what has happened."

"Are you sure you don't already know? It seems you haven't been truthful with me . . . with us, about what's going on around here. I find particular offense to you wanting detailed information about me given to you in secret. I think it's becoming obvious to all of us that your gestures of friendship aren't so friendly after all and I'm feeling particularly used right now." John was watching her closely for any reaction while simultaneously watching the entire room for signs of trouble.

Helia's expression hardened and her lips pulled thin. "You have no right to talk to me like that Colonel. You are obviously upset about your friend's injuries, so I'll excuse your behavior and tell you again that I will discuss this with you at a later time."

John caught movement in his peripheral vision and turned to see Savill and two of his men heading down the corridor toward the infirmary door. John concentrated for a second and the door to the room slammed shut. "We'll talk now," he said, his voice hard.

The infirmary had gone silent, with everyone turning to stare at the doors. Pounding from outside confirmed that the doors had been locked. Carson and Emira looked at one another before turning their attention back to their patient and the nurses took the hint to get back to their duties.

Helia frowned at John. "How did you do that?"

John was aware that even Ronon, Teyla, and Elizabeth were staring at him in disbelief, but he pushed down the uncomfortable feeling to focus on the matter at hand. "I simply asked Atlantis. I keep telling you, this is my city too."

"Captain, we'll have you out of there in just a minute." The voice sounded like Savill's, even though it was being shouted through the closed doors.

"Tell him to back off and give us a few minutes and I'll open the doors when we're done." John made it clear he wasn't asking.

Helia hesitated. "How do I know I can trust you?"

John laughed and it came out sounding slightly crazed. "You are asking me about trust? You have to be kidding me. I'll tell you what, never mind." He closed his eyes a few seconds and then opened them. "Now we can talk."

Helia looked frightened, her eyes wide. "What have you done?"

Elizabeth grabbed his arm, clutching him desperately and her eye pleading. "John?"

Only Ronon looked pleased and John sighed at their assumptions. "Relax. No one is hurt, she just put them to sleep to keep them from disturbing us. The same will happen to anyone coming down this corridor, so you may want to call off any other people you have coming."

Helia got on her radio to the control center, telling them she was unharmed and not to send anyone else. She then looked back at John. "What has happened? Why are you doing this?"

John crossed his arms and looked at Ronon, who nodded and turned to Helia. "Teyla and I heard you talking with Emira after Sheppard left the chair room. We were around the corner." Teyla nodded her support of his story.

"Then Rodney is almost blown up in his . . . in the lab and it seems it was done on purpose. So we have people trying to maim or kill Rodney and you keeping secret tabs on my test results. I want an explanation or we walk out of here. But I may have to have a little talk with Atlantis before we leave." John smiled, but there was no humor or good will in it. It was dark, threatening smile.

Elizabeth shuddered with the memory that John had a dark side, one that she had secretly hoped she'd never see again. But they had pushed all his buttons. They had injured his friend. They had manipulated him and taken away his control. They had lied to him and betrayed his trust. She hated to admit it, but she was a little bit afraid.

Carson and Emira walked over to join the party. Carson nodded to them. "Does anyone care to fill us in about what is happening over here?"

John let his eyes dart over to the doctors. "How's Rodney, Doc?"

Carson frowned at John, but said nothing about the fact that the pilot had disconnected the monitors. "He'll be fine. He has some first and second degree burns on his arm, shoulder, and face. He'll be in a bit of pain for a few days, but there shouldn't be any lasting effects."

"So his eyes are okay?" asked John, his voice deep with worry.

Carson smiled. "Aye, they are. All the damage is external."

John nodded, relief filling him. He smiled when he heard Rodney call from across the room.

"Hello? Where did everyone go? Injured man here."

"Keep your pants on, Rodney, we'll be right there," yelled Carson over his shoulder before turning back to the group. "Well, I'd better get back to Rodney and you can let me in on what's so all fired important later." With that, he turned and went quickly across the room to his patient. Emira turned to follow.

"Emira, wait, I'd like you to stay," said Helia.

Emira looked surprised for a second, but then nodded. "As you wish, Captain."

Helia took a few deep breaths and then leveled her gaze at John. "I'll tell you everything. You deserve that much. But please don't blame Emira or anyone else here for my mistakes. I'm afraid I let personal feelings get in the way of my good judgment, something a good leader should never do." She rubbed her hands together and paced a few steps before she seemed to find a good place to begin.

"There are stories, in our history, that every few generations there comes an individual with special abilities, a deep link to the city that allows them to almost become one with Atlantis. I heard these stories as a child and did not believe them. I thought them foolish and impossible." Helia paused and put one hand to her mouth, as if holding back a flood of emotions. Within a few seconds, her face returned to its emotionless mask.

"Until my brother showed me otherwise."

John's head shot up and took a deep breath as he felt his heart suddenly being to race. "Your brother?" Even as he asked, he felt Atlantis touch him with her memory of him.

"Yes. Celeres was my older brother. He . . . also possessed a connection to Atlantis that was unusually strong, not unlike yours. When he finally told me of it, I did not believe him until he showed me. After that . . . I was a bit jealous, always trying to achieve a connection of my own. He loved her dearly, as you seem to. I think I was afraid he loved her more than he loved me." She stopped and crossed her arms, hugging herself in a way that made her seem vulnerable.

John sensed a sadness in Atlantis that sent a shiver down his spine. Atlantis had loved him too, at least in her own way. "How did he die?" he asked quietly.

Helia whirled around and stared at John for a few minutes before schooling her expression and nodding. "I should have expected that. She remembers him then?"

John nodded. "She does. And I can tell she was very fond of him."

Helia smiled a small, bitter smile. "As was I. Celeres joined the military and became one of their best pilots, ironically enough. Soon afterward, he revealed his abilities to our parents and to the High Council. They discovered that he could accomplish things from the chair that no one else could. Sound familiar?" She let out a small, strangled laugh as she looked up at John.

"Although as far as I know, she never hid him from the sensors. I guess she's learned a few new tricks over the years."

John smiled. "Maybe he just never asked her."

Helia seemed to relax a little as she and John held the other's gaze. "I suppose that is possible." She stood silently for a few moments before continuing. "The council did not want my brother to fly missions any more, thinking he was too valuable an asset, but he would not be denied. He loved to fly more than just about anything."

Elizabeth looked up at John, seeing the acceptance in his eyes as he listened. Things that had previously made no sense were now beginning to click into place. No wonder Helia had been so fascinated by John's connection.

"He was killed in a battle with the Wraith, trying to protect Atlantis. He died for her . . . and for us." She walked slowly over to John and looked up at him. "Celeres looked nothing like you and yet, he had that same look in his eyes when he talked about Atlantis that you get. The only other person I've seen talk about Atlantis as if she were a living being instead of a city is you. In that respect, you reminded me of him and made me want to understand the connection better. I think I was trying to grasp some of my brother through you and . . . now I know how wrong and misplaced that was." Her expression sobered as she looked away. "I have been foolish in my actions and I hope you will not hold others responsible. Emira was merely following orders and Savill is trying to protect me and the city."

John closed his eyes for a second before taking a deep breath and moving closer to Helia. "Do you trust me?"

Helia looked up at him, surprised by the question. Embarrassed, she looked down at the floor. "Yes," she whispered. "I do trust you."

John smiled and nodded. "Then come with me." He walked toward the doors, which opened as he approached. They walked out into the hallway, where Savill and the two men that had been with him were sitting up and rubbing their heads.

"They'll be okay," he said to Helia, who walked beside him. "It was just a little stun." Elizabeth, Ronon, and Teyla, walking behind John and Helia, exchanged a questioning glance. None of them had been aware such a thing was possible.

They arrived at the chair room a few minutes later and John sat in the chair. "I've never tried anything like this and I don't think Atlantis has either, so we aren't sure it will work. Helia, come here please."

Helia walked over to stand beside the chair. "All right, what now?"

"Give me your hand." John held out his hand toward her.

Helia nodded and put her hand in John's. He nodded, recognizing her trust. Turning his wrist, he placed her hand on the gel-like hand rest with his on top and his fingers stretching between hers to contact the chair. Leaning back and activating the chair, he closed his eyes. "Close your eyes and clear your mind. Think of a blank slate."

John connected with Atlantis and within a few seconds, scenes of Helia and her brother at a much younger age filled his mind. "Oh, my," she said softly, letting him know that she was seeing it as well. For the next several minutes, Atlantis took them through various times in Celeres life, some happy and some not so happy. Throughout the impromptu show, a feeling of care and love permeated both John and Helia as the city's devotion to one of her own bled through. When it was finished, the chair darkened and John sat up.

Helia pulled her hand away and quickly wiped a tear from her cheek. "Thank you," she said roughly, clearing her throat. "You have shown me a great kindness, especially in light of my actions."

John smiled as he stood, swaying slightly. "I understand better now. I do wish you had been honest with us."

"As I should have been. I understand if you wish to leave, as that is twice I have not honored your trust, but I hope you'll stay. I give you my word that there will be no more secrets or dishonesty."

"It will have to be a group decision," he said just before dropping heavily into the chair.

"John?" said Elizabeth, stepping forward to place a steadying hand on his arm.

John closed his eyes against the dizziness and weakness that gripped him. He knew what he had done had been risky, but it had seemed worth it. "I'm okay, just a little tired." He opened his eyes to find what seemed like a room full of worried looks.

Helia took a deep breath and put her hand on John's other shoulder. "You have given me a great gift, but I fear we should get you back to the infirmary. And I must find out who booby-trapped Dr. McKay's work station."

"I want in on that investigation," said John. "You don't mess with my friends like that."

Ronon snorted. "And what makes you think Beckett will let you out of the infirmary after he hears about this?"

John grinned slyly. "You know, nothing says we have to tell him about this. I'm fine, guys, really." He stood up, grabbing the side of the chair as the room seemed to tilt sickeningly to the right.

"Nice try, John, but I don't think so," said Elizabeth, reclaiming her hold on John's arm.

Helia nodded as she took his other arm. "And I just promised to be honest and not keep secrets. I plan on keeping my word."

John sighed and looked hopefully at Ronon and Teyla, who were smiling. "_Now_ she decides to be honest."

TBC

Okay, the bad news is that I have caught up with myself, so new chapters may be a couple of days apart. I promise to write as quickly as I can in between work and softball practice/games/tournaments. Thanks for the continued reviews!!


	11. Chapter 11

The Return Part 2: Favorite Son - Chapter 11

John lay on his left side, watching the rhythmic rise and fall of Rodney's chest. He hadn't put up too much of a fight when Carson insisted he spend the night in the infirmary for observation. He hated being stuck in here again, but he hadn't minded the chance to keep an eye on Rodney and make sure he was okay. He was well aware that the scientist had gotten off easy.

"Colonel, can I get you anything?" John recognized the soft voice as that of Marna, one of the nurses. He lifted up to lean on his elbow so he could see her better. She was about Teyla's height, with dark hair and equally dark eyes, but a bright smile.

"No, I'm good." He smiled easily, appreciating her concern. He knew it was late.

"Dr. Beckett left instructions for something I could give you to help you sleep if you needed it. He thought you might be . . . wound up after what happened earlier."

John chuckled. "Wound up, huh. I see he's indoctrinating you with Earth expressions."

Marna smiled. "Yes, he explained the meaning when I told him I did not understand."

"Well, thanks, but I'm fine. I'll drift off in a little while. Any word on finding Renato yet?"

"Yes, actually, we just received word from Savill that they have him in custody. He told me to pass the word on to you if you were awake. He hasn't confessed yet, but they have just begun the interrogation process."

John sighed and frowned. "I'd love to be able to help with that."

Marna smiled and patted his arm, similar to the way Carson did when he was in what John called his comfort mode. "Now, you need to rest, Colonel Sheppard. Savill will handle Renato, you can be sure of that." She pressed on his arm until he lay back against the pillows and then she proceeded to tuck the covers in around him. John resisted the urge to make a sarcastic comment, not really knowing if it would hurt her feelings. If any of the Earth nurses had done this, they would have already heard from him about the mothering.

"Done?" he asked when she finally backed away from the bed.

"Yes, now you'll be nice and cozy. Let me know of you need anything." Marna smiled sweetly, gave a short nod, and left. As soon as she was out of sight, John pulled the covers loose so he could move around more freely and then glanced over at Rodney.

"She's gone, you can quit pretending to be asleep now."

Rodney carefully cracked one eye open and then the other, breathing a sigh of relief. "Good, I didn't want her tucking me in too."

"Uh, thanks for the support." He studied the scientist carefully. Rodney's face was a bright red and his eyelids looked swollen, almost as if he'd had a marathon crying session. His right arm was bandaged and in a sling and an IV entered the back of his left hand. "How do you feel?"

Rodney snorted. "Like someone blew me up, how did you think I'd feel?"

"Are you in much pain? I could call Marna back."

"Heavens, no, don't do that. It hurts, but in kind of a fuzzy, weird way. I think I still have a pretty good buzz going from the last dose, so I'll be okay for a while."

John nodded as he continued to stare at the scientist. Rodney finally looked exasperated. "What? Why are you looking at me like that?"

John felt the corners of his mouth twitch, in spite of his efforts to control it. "I was just noticing your . . . missing hair?"

Rodney frowned in obvious confusion, running his good hand up through his hair. "My hair is fine. What are you talking about?"

"No one told you? Not Carson or one of the nurses or Emira?"

Rodney stared at John. "Told me what?" he asked, tilting his head slightly.

John bit his lower lip to keep a straight face. "You, uh, have no eyebrows."

Rodney sighed and rolled his eyes dramatically. "Don't be ridiculous," he started, reaching up to gingerly touch his scorched face above his eyes. In truth, he still had a few hairs above each eye, but not enough to be classified as an eyebrow. He let out a loud breath and closed his eyelids. "Well, isn't that just great?" he drawled sarcastically.

"It'll grow back . . . in a few weeks," John said, chuckling lightly under his breath.

"You're going to be incorrigible, aren't you?"

"You better believe it."

Rodney groaned loudly. "I'm so screwed," he mumbled. After a few moments, he suddenly turned his head back to John "Did she say they caught Renato?"

"Yep. Savill is questioning him now."

Rodney nodded, looking up at the ceiling. "I hope he's the one who did it. I'd hate to think the real guy is still out there gunning for me. Plus, I have no idea who else it could be. Tweedle dee and tweedle dum aren't very happy with me right now, but I honestly don't think they have the brains between them to set this up."

John stared. "Tweedle dee and tweedle dum?"

"Yes, the two lab minions that Helia stuck me with. I never thought I'd miss that motely crew from Earth, but I think even Kavanagh has these guys beat."

John had raised up on one elbow and he shook his head and sighed deeply. "You should write a book, McKay. How to make enemies and convince people to kill you."

Instead of looking upset, Rodney just turned his head slightly so he could see John's face. "No, I think you already have that subject covered."

John opened his mouth to protest, but then changed his mind. "Touché. And it _was_ Renato."

Rodney started narrowing his eyes to frown at John, but it pulled on his burned skin too much, so he gave up. "And you know this how?"

"Atlantis. She basically sees almost everything. It was just a matter of going back through her . . . . memories, for lack of a better word, and accessing that information. If Savill doesn't get his confession by tomorrow, I'll just have her send the proof to Helia and Savill. Either way, he shouldn't be blowing anyone else up."

"Good to hear," Rodney said quietly, the relief evident in his voice. "So why are you here? What did you get yourself into this time?"

John gave a short laugh, knowing Rodney would be amazed at all that had happened. He briefly told him about what Teyla and Ronon had overheard and about Helia's confession. He then moved on to what he and Atlantis had done from the chair and the effects it had. Finishing his story, he told Rodney that the group was to meet the next day to discuss what they wanted to do.

"What do you want to do?" asked Rodney.

"I've been thinking about that for a while now. I think I still want to stay. I understand Helia's actions a lot better now. Even though they weren't appropriate, I don't think she meant any harm. I'm liking the Ancients more, the better I get to know them. Well, most of them anyway," he grinned.

"Well, you did say earlier that you weren't sure you could leave."

John frowned, looking uncomfortable. "Look, about that. I may have been a little . . . overly dramatic with that. Atlantis was just so . . . intense those first few days we were back, it was overwhelming. It's back sort of like it used to be now. I mean,, the connection is stronger and I'm more aware of her now, but it's not so encompassing as it was."

"So, you could leave if you wanted?"

"Yeah, sure. I would miss her, like before. But if this had continued the road it was headed down, I was ready to say let's go home."

Rodney let out a deep, slow breath. "I'm glad. You kind of had me worried."

"What about you? Stay or leave?"

Rodney hesitated. "I'm not sure yet. Maybe stay, if Renato is out of the picture and if we think Helia will really start playing it straight with us. Did anyone else voice an opinion?"

John punched his pillow, trying to fluff it up. "No, they didn't really have a chance. Carson pretty well threw them out so he could do a scan and check me over. You'd think I'd just wrestled with Godzilla or something."

"Dr. McKay, Colonel Sheppard, you are both supposed to be sleeping."

Both men jumped at the sound of Marna's stern voice. Neither had been aware of her quiet approach as they focused on the conversation and their future.

"Now, are you going to stop talking and go to sleep, or should I call Dr. Beckett?"

"He started it," said Rodney, before he even thought.

John shot a sideways glance at the physicist. "Gee, thanks Rodney. Throw me to the wolves, will ya?" 

Marna put her hands on her hips and looked sharply at John. "And just what are wolves?"

Rodney cleared his throat and began adjusting the covers. "You get yourself out of that one, I'm going to sleep like a good patient."

oOo

John sat on the edge of the bed, fully dressed and his legs swinging back and forth. "How much longer, Doc?"

Carson turned away from securing the sling around Rodney's neck. "Colonel, you're almost as impatient with others getting released as you are with yourself. I'll be finished when I'm finished and I will not be rushed. Either be quiet or go wait somewhere else."

John grinned at Rodney, who was grimacing at the doctor's ministrations. "Sorry, Doc, I'm just hungry." It was almost lunch time and his stomach was beginning to growl. He'd been released over an hour ago and had offered to wait on Rodney so the three of them could join the others for lunch.

Carson stepped back from Rodney, also dressed and sitting on a bed. "How's that?"

Rodney shifted around a bit, wincing at the pain it stirred. "It's okay, I guess. My arm really hurts, Carson, are you sure you can't give me something stronger?"

Carson sighed. "If I give you anything stronger, you'll be laid out and probably have to stay here."

Rodney grunted. "Fine. Can we go now? I'm hungry to and it's going to take me forever to eat with my left hand."

Carson gave John a look that said all his patience was gone. "Yes, you can go, the both of you. I'll join you in just a few minutes. I need to make sure Emira knows where I've gone."

"We can wait," offered John.

"No, go on. Rodney will need help with his tray. I'll be along in a minute."

John shrugged his shoulders. "Okay, Doc. We'll save a seat for you."

Carson grinned. "Good. Now off with you both so I can get out of here soon to join you."

Several minutes later, John was setting Rodney's tray on the table and then going back for his own. By the time he returned and got seated, they saw Carson entering the mess hall. It wasn't long before the whole group was assembled and digging into the food.

"I am glad to see you looking better," said Teyla, sitting across from Rodney.

Rodney nodded as he finished chewing. "Better being a relative term."

Teyla looked a bit confused, but said nothing. She glanced at Ronon and saw him staring at Rodney's face and grinning. Silently, she nudged the side of his leg with her foot. When he looked at her, she shook her head slightly. Ronon just returned to his grinning.

"Is everyone caught up on recent events?" asked Elizabeth. She was addressing the whole group, but looking at Rodney since he'd been busy getting treated during a lot of it.

"Sheppard caught me up, I think," said Rodney. "Do we know whether Renato confessed or not?"

Elizabeth nodded. "Yes, I met with Helia and Savell before I came here. Renato finally admitted rigging your station to explode when you hooked up your computer and turned it on. He claims he just wanted to scare and embarrass you and didn't realize how dangerous the explosion would be."

"No one is falling for that, are they?" asked Ronon, pausing between bites.

Elizabeth gave a slight head shake. "No, they aren't. Although from what was said, I doubt he actually intended to kill Rodney, he knew that serious injury was not only possible, but probable."

"Why?" asked John, feeling the anger build in the pit of his stomach.

Elizabeth sighed and set her fork down. She looked directly at Rodney as she spoke. "He was angry and jealous. He thinks the Ancients are superior to us in every way and he couldn't understand why Helia let a mere human in his lab, much less gave him free reign and his lab station. He made it clear that we have no place here and should be sent back to Earth immediately, that we have nothing to offer."

Teyla bowed her head. "It is sad when someone is so closed to those around them that they are unwilling to see the possibilities there. What will happen to him?"

Elizabeth shrugged her shoulders. "They haven't decided, long term. For now, he's in Steve's old cell."

They ate in silence for several minutes, just enjoying the company of their friends. John finally looked around the table. "What are we going to do? Are we going or staying?"

Ronon chuckled. "Seems like we just had this conversation."

Elizabeth laughed and nodded as she stirred her fork around in something that looked like cheesy mashed potatoes. "That's because we did. What's the decision this time around?"

When no one else said anything, John cleared his throat and began. "I want to stay. Maybe give them one more chance. I know they haven't given us much cause to trust them, but I think it's been bad judgment and not bad intentions. If we really are past that, this could still work out well for us."

Ronon and Teyla looked at one another before glancing back at John. "Ronon and I discussed it at length this morning. We were also of the opinion to give it one more try."

Ronon nodded, but pointed his fork at the group decidedly. "One more betrayal, one more sign that they won't keep their word, and we're leaving."

Carson nodded, looking almost relieved at the discussion so far. "Aye, I agree. Let's give them one more chance."

Elizabeth looked at Rodney, poking his food and looking uncomfortable. "Rodney, you haven't said much."

"And that alone has us worried," said John, trying to lighten the mood.

Rodney stopped and looked up at the group, taking a deep breath. "I can stay if the rest of you do."

"Renato is an isolated incident and Savill has it covered," said John. "You should be okay now. At least as safe as we ever were here."

Rodney smiled a little. "Safer actually. We have 3 ZPMs now. Full shield and weapons."

John nodded and smiled. "Right." He looked around at the former expedition leader. "That just leaves you, Elizabeth."

Elizabeth nodded. "I say we stay. One last chance to get this right."

Ronon looked down at his plate, a smile stretching across his face. "We should at least stay long enough for McKay to grow his eyebrows back."

oOo

The whole group went to Helia's office after lunch. They crowded into the small room, an act that seemed to make her nervous. She stood as the each found a place to stand, with John and Elizabeth in the front. "I assume you have reached a decision."

Elizabeth nodded. "We have. We're staying, at least for now. But we all agree that enough has happened that we will leave at the next sign of mistrust or betrayal."

Helia nodded. "I understand. I'm glad you have decided to stay."

"We're trusting you and we expect you to trust us back," said John.

Helia gave another nod and a small smile. "I've worked through my issues, Colonel Sheppard. There will be no more problems. As a matter of fact, I was just talking to Emira and she tells me that she and Carson have made some discoveries that they would like to share with all of us. I thought we could meet in the conference room. It might be a little less crowded."

Murmurs of agreement went through the group, now starting to sweat at the close proximity of their neighbor and the lack of air circulation. "When?" asked Elizabeth.

"We can meet now if you are able."

"Now is fine," responded John, feeling nervousness begin to build, making his stomach churn. He wasn't sure he wanted to know the results of their tests and he was definitely uncertain about having it shared with others.

"Good, I'll contact Emira and let her know so she can join us."

Elizabeth smiled and nodded. "We'll wait for you there." At her words, the group began to move out into the hall and toward the conference room a few feet away. A few minutes after everyone was seated, Emira entered with her data pad and took a seat between Carson and Helia.

"Emira, why don't you and Carson tell us what you've discovered."

Emira nodded and glanced over at Carson, who gave her a smile and a small nod. Emira looked across the table at John. "Colonel, we've been studying your test results and we've made some interesting discoveries. We've actually found three regions of DNA that are active when you are communicating with Atlantis. One of those is the ATA gene, which all of us have and some of your people. That is what is necessary to activate most of the general systems and things like the gate ships. There is a second area that most of us have and a few of your people have, that allows a more intense connection and a few more things to be activated. Carson also has this second gene. Dr. McKay, you do not because no one knew about it to include it in the gene therapy."

Rodney nodded and looked deep in thought, as if he was putting a puzzle together. "I'll bet O'Neill has it as well. That's why you guys can do things others can't."

"Aye," said Carson. "But it's this third gene that has us baffled. We can't find it in anyone else. None of the Ancients here have it and there's no reference to it in the data base. We think it's possible that this third gene is the source of the stories Helia heard about some individuals in their history having special abilities to connect to the city. It's even possible that her brother possessed it."

"Can you make your gene therapy with this third gene?" asked Helia.

Carson shrugged his shoulders. "I don't know. It has a peculiar structure, with alternating repeating and non-repeating segments. We believe an individual would have to have all three segments to achieve the level of interaction Colonel Sheppard gets. We can try to develop one, I'm just not sure of the success."

Helia nodded. "All right, what else?"

"Well, the Colonel develops an odd pattern of brain waves when he's connected to the city, but we have nothing to compare that too. I'd like to run an EEG on some of your people as well as myself and Rodney to have a basis of comparison."

Helia nodded. "I see no problem with that. Savill has the strongest connection of those of us left and I know he would cooperate. I'm sure we can find a few other volunteers."

"Thank you," said Carson and Emira at the same time.

"Carson, did it look like the problems with chair were cleared up?" asked Elizabeth.

"Aye, I believe they are. Colonel Sheppard is cleared to work from the chair when needed, but I'd like to look him over if he's in there for very long or he has any problems." Carson gave John a stern look until the colonel nodded his acceptance.

"Good," said Helia, looking satisfied. "Emira, you and Dr. Beckett are cleared to run the EEG on our people. Let me know if you have trouble getting cooperation. And please be working on that gene therapy so that we can have more people able to connect with the city on the same level as Colonel Sheppard. Is there anything else?"

No one said anything, so Helia nodded. "Dr. McKay, I would like to offer our apologies for Renato's actions and I can assure you that he will be punished. I'm glad to see you are able to be up and around. And I would like to meet with Colonel Sheppard, Ronon, and Teyla in the morning to discuss your first mission. If there is nothing else, then we are finished." Helia paused a moment and then looked across the table.

"And Dr. McKay . . . that is an interesting new look you have. Very unusual."

Rodney sighed and let his head drop forward. "I'm going to kill Renato," he mumbled.

TBC


	12. Chapter 12

**NOTE: **I'm SO sorry about the delay. School is crazy right now and I'm even crazier. I'm doing my best, I promise. And yes, there is more Shep whumping on the horizon with a slight nudge in that direction this chapter.

The Return Part 2: Favorite Son - Chapter 12

Elizabeth stood in her old spot by the railing, watching the active stargate for the return of her best team. It almost seemed like old times, except for Helia standing next to her and that she didn't really know the Ancients at the controls. She caught herself listening for Chuck to feed her information, but he wasn't there. She missed that.

Ronon and Teyla walked into the gateroom, laughing as they moved across the room. Two Ancients came through next, their expressions bland and unconcerned. At least there was no sign there had been trouble. Savill and John came through last, with John nodding his head as if he'd been agreeing to something said on the other side of the gate. Elizabeth felt her shoulders sag with relief. Even though it had been planned as a simple bargaining mission with people they had previously traded with, she'd learned the hard way that no trips were guaranteed to be safe in the Pegasus Galaxy.

Elizabeth followed Helia down the steps to meet the incoming team. She pushed back the resentment she found curling within her at having to follow another around what had been her city. Swallowing hard, she tried to remind herself that Helia and her people were here long before her and the expedition from Earth.

"I'm glad to see you have returned safely," said Helia. "Did it go well?"

John and Savill grinned at one another and then John nodded. "Yeah, it went very well. They were agreeable to trading anyway, but when they found out it would be helping the Ancestors, they got really excited."

Teyla gave a small nod. "The Chartarians will have some baccarupia root to trade within a few weeks. They said if we can truly help them with their irrigation problems, they can increase their crops and provide us with a larger amount."

Ronon grinned and crossed his arms. "Plus, they all of a sudden wanted to add in some daria fruit."

Elizabeth's expression showed her confusion. "Daria fruit?"

John nodded enthusiastically. "That's a good thing, believe me. Those things are really good."

Teyla raised one eyebrow. "As was apparent by the large amount you and Ronon consumed."

John frowned in a mock look of hurt. "Hey, Savill ate some too."

"Yes," Teyla agreed. "Just not as many."

Savill patted his stomach as he grinned slyly. "I'm afraid if I ate as many as these two, I'd soon be too large to fit through the gate. I can't afford to get fat and slow, as that can be deadly."

Elizabeth did her best to hide her smile behind her hand. Helia wasn't grinning like her, but even she looked amused. "John, you and Teyla and Ronon need to check in with Carson for your post mission."

John put his hands on his hips and a smug expression on his face. "You know, we were just talking about that. Savill tells me that the Ancients don't have to have post mission exams. I think we should follow their lead on that."

Elizabeth looked at him for a moment before speaking. "Well, the last I checked you weren't an Ancient and you aren't even originally from this galaxy. There is still a lot we don't know and it doesn't hurt to be safe. The post mission exams stay for all of our people." She took a moment to glance at Ronon. "Yes, Ronon, that includes you too."

John returned her gaze for a moment and then shrugged his shoulders. "Can't blame a guy for trying."

"Actually, I can," she said playfully.

Helia cleared her throat loudly. "I suggest we all meet in the conference room to discuss the mission after the evening meal."

Elizabeth smiled and nodded. "That should give you plenty of time to get checked and eat." She turned to John. "Beckett. Go. Now."

John motioned at Teyla and Ronon. "Come on guys, we might as well get this over with. Maybe someone hid the needles."

oOo

Carson cleared the team in almost record time since there were no injuries. He had been relieved to hear about the peaceful mission and the successful trade agreement. The team had then joined Rodney and Elizabeth in the mess hall for dinner. Rodney's arm was still in a sling and his face still red, but the bright color was beginning to fade. Ronon and John managed to go through the whole meal without teasing the scientist, much to everyone's surprise.

Once in the conference room with Helia and Savill, the team settled in to make their report and Rodney came to listen. He'd been partly relieved and partly disappointed to have been grounded and missed the first mission. After listening to Savill, John, Ronon, and Teyla's account of the trading activities, he decided to go with relieved.

Helia addressed the group when the discussion drew to an end. "I am happy to see that our people and yours were able to work together so well. I think it might be a good idea to continue these joint missions for a time. It not only provides an opportunity for both sides to see how the other works, but I believe it will also build trust and respect between us."

Savill nodded. "I agree, I think it will give us an opportunity to see each other in the field. That is the place to really see how a soldier thinks and reacts. When you trust them with your life, everything else is much easier."

"I have no objections," said John. "I think we can learn from each other. That might just make the difference in our survival down the road." He turned to the other members of his team. "Ronon, Teyla, what do you guys think?"

"I have no objection," said Teyla. She dipped her head forward slightly toward Savill. "I thought the mission was enjoyable."

"I don't have any problem with them coming along," said Ronon. "He's right about one thing. What a person does in the field while under attack, that will tell us who knows what they're doing and who doesn't."

Helia let out a small breath. "All right, it is decided. Missions will be joint ones until further notice. Savill, you can determine who will accompany you from our people. Now we should discuss when and where the next mission will be."

Rodney cleared his throat loudly. "Uh, if I may, I have a suggestion. Dolon and I made a lot of progress today and we could use the Colonel to sit in the chair for a few days. I think he has some repair teams lined up but we need someone operating the chair to really get the repairs going in the right direction."

Helia looked surprised, but pleasantly so. "Yes, by all means. I did not expect you to be ready for him so soon. You and Dolon work well together."

Rodney shrugged one shoulder. "Amazingly . . . we do work well together. He just ignores me when I insult him and occasionally insults me back. Reminds me of Zelenka a little bit. We could really make some headway if Radek was here."

Helia frowned a little. "Who is this . . . Zelenka? Was he here in Atlantis before?"

"Yes, he was the second in command of the science department when you kicked us out of Atlantis. No offense."

"Perhaps we could discuss the return of a few scientists soon. Discuss with Dolon any need for more people to help you with repairs, as well as future maintenance of Atlantis. When you have decided what your needs are, bring them to me and I will consider letting your friend and a few others return."

Rodney gave a small nod and his expression lightened. "Okay, we can do that." He seemed pleased with the prospect of bringing some of his people back.

"What do we do while Sheppard is in the chair?" asked Ronon, frowning as if he already knew the answer.

"What do _you_ want to do?" asked Elizabeth, a small smile on her lips. She knew Ronon liked to sit still about as much as John did.

"Why can't Teyla and I accompany Savill and his men on a few missions. There's no reason for us just to sit around when there's so much to be done."

Teyla raised her eyebrows slightly and then looked at Helia. "There are other planets with which we had trade agreements for food and other supplies. Perhaps we could reestablish a connection with them as we did with the Chartarians."

Savill rubbed his chin as if considering the idea and Helia watched him, waiting on his opinion. He finally dropped his hand and nodded. "I think it's a good idea, if Colonel Sheppard has no objection."

John shrugged his shoulders. "No, I think it's a good idea, as long as you stick to planets we've visited before and they've proven friendly. No use in all of us being stuck here I guess."

"All right, Dr. Weir, you work with Teyla and Ronon to develop a list of prospective planets. We'll meet tomorrow to discuss your suggestions. Colonel Sheppard, I'll leave you to help Dr. McKay and Dolon with the repairs from the chair. I would appreciate it if either Dr. McKay or Dolon could brief me at the end of each day on what has been accomplished and what is planned for the next day. Dolon is working with one of our engineers, Lycus, about the physical and structural repairs. Is there anything else?"

When no one said anything, Helia nodded. "I will leave you all to your duties then."

As they stood to leave, Rodney looked over to John. "I'll meet you for breakfast at 0700 and then we can get to work."

John grinned broadly. "I can honestly say I'm looking forward to it." As John left the room, he ran one hand along the wall, feeling the pull from the other side. _See you tomorrow, _he thought.

oOo

It was five days later before the team was able to get together again. Elizabeth arrived at the mess hall for supper about the same time as Carson. They went through the line together and selected a table that would be big enough for the whole group once everyone arrived. Elizabeth glanced at Carson once she was settled. "Have you seen Ronon and Teyla since they got back?"

"Aye, checked them both out and they're fine. I believe they went to get cleaned up before joining us."

"Good. They said the mission went well and the Illarions are willing to resume trading."

Carson paused and looked at her, frowning. "Illarions. Are they ones with the beans the cooks used to grind up and use like cocoa?"

Elizabeth grinned. "That's them. We'll have to show the Ancients the fine art of making chocolate cakes and such."

"I do miss chocolate," said Carson longingly.

"Me too. How's the gene therapy coming? I haven't seen much of you or Emira the last few days."

Carson grimaced and set his fork down on the edge of his plate. "I'm afraid I have some bad news on that front. We've been unable to make a therapy using either one of the two new genes. Gene two seems to be working right up until we inject it into something to test. The third gene, well, I've never seen anything like it. It begins deteriorating the second we cut it out. It's like it can't survive unless the whole chromosome is in tact, and of course we can't make a gene therapy like that. Emira and I have tried everything, but nothing works. I think Emira is going to arrange a meeting with Helia tomorrow to let her know. She won't be happy, I'm afraid."

"No," Elizabeth agreed. "She won't. Well, you did your best. Maybe there's a reason it's like that."

"Aye, we've thought of that. The more operating genes you have, the more power you have. We probably wouldn't want someone like Renato having the same power over Atlantis as Colonel Sheppard."

Elizabeth nodded. "Definitely not."

They both looked up as Ronon and Teyla joined them. As they settled in their chairs, Rodney came through the doorway and took his place in line, joining them a minute later. He paused as he set his tray down.

"Where's Sheppard?"

Elizabeth narrowed her eyes at the scientist. "You're the one who's been working with him all day. Why don't you tell us?"

Rodney shrugged his shoulders as he sat down. "He left a few minutes before me. I was trying to clear up some stuff with Dolon. I really thought he'd be here by now."

"There he is," said Teyla, nodding toward the doorway, where Sheppard leaned against the wall. His face was pale and he carried about two days worth of beard growth. Dark circles under his half-lidded eyes made him look completely exhausted. Pushing away from the wall as if it took all his energy, he shuffled to the line to pick up a tray of food and then stood looking for the team. He looked at them several times before it seemed to sink in that he'd found the people he was looking for. He ambled over to the table and sat down in the open seat.

"John, are you all right?" asked Elizabeth.

"Fine," came the slow, almost sleepy response. John picked up a fork and poked it into the food on the tray, but made no effort to lift it to his mouth.

"Colonel, you don't look fine," said Carson, his face lined with worry. "When have you slept?"

"Last night. I'm okay, just tired."

Carson shook his head and clenched his jaw. "How long were you in the chair and how many days have you been working down there?"

John shrugged his shoulders. "Few hours."

Carson wasn't satisfied with the vague answer. "How many is a few? Rodney?"

Rodney's eyes went wide as he looked up from his plate. "Why are you asking me?" he said in a high pitched voice.

"Because I assume you were calling the shots on this little project and you are probably the one telling Colonel Sheppard when to activate the chair. If you can't remember either, maybe I could see if Dolon or someone could check the computers for me. I'm sure there is a way to confirm how long the chair has been active over the last few days. How many days have you been down there?"

Rodney sighed and huffed a few times before giving in. "This was our fifth day. We've been working six or eight hours usually, except . . . maybe ten yesterday." The last few words were spoken so softly they were barely audible.

"Ten hours?" Carson boomed. "In one day? Are you both bloody daft? What possessed you to do that?"

Rodney straightened and set his hands on the table, his posture taking up the defensive. "Yesterday was important. We got power restored to the second chair and accessed all kinds of systems we didn't even know existed. Well, Dolon knew, but none of us knew because we didn't have three ZedPMs to work with. We were able to restore power to several new sections and get a lot of repairs accomplished."

"And all of this needed to be done in a single work session? Did it need to be done yesterday?"

"The sooner the better Carson," said John wearily, his shoulders sagging as he sat hunched over his food. "We need to be ready for the next attack, be it Wraith or Replicator. We do what we need to do. I'm just tired, like we all get tired when we work hard. Sometimes it has to be done."

Carson shook his head as he pursed his lips. "No, I'm not buying that. This is not like the siege, when attack was imminent. This could have just as easily been spread out over a couple of days if either one of you had any sense. And Rodney, look at the man. Did you not notice he was dead on his feet?"

"Hey," John said sharply, glaring at Carson.

Rodney frowned and poked at his food. "Well, Dolon did mention he looked kind of tired, but I thought he'd say something if he needed to rest."

Elizabeth cringed. "You honestly thought John would tell you he was tired and needed a break?"

Rodney shrugged his shoulders and looked down. "You know how I get when we're working on something important. I don't think about anything else."

"Don't get mad at Rodney," said John. "His tendency to totally focus on his work is why he's able to pull together the stuff that he does and it usually ends up saving our lives. It's my fault. I just got caught up in working with Atlantis and it was exciting to see the city being repaired. I guess I didn't realize how much it was taking out of me. All I need is some sleep and I'll be fine."

"Well, I'd like to be certain of that. Colonel, finish eating and then you'll need to come with me."

John set his fork down and pushed the tray away. "I'm done."

Carson studied the near full plate and then the Colonel. "When was the last time you ate?"

John looked at Carson blankly a moment before lowering his gaze. "I'm not sure."

Carson looked aggravated, but not surprised. "Well, did you eat lunch?"

"No."

Rodney groaned and shook his head. "That was so not my fault. We quit to get lunch and Dolon and I hit one of the other labs to check on something before we went to the mess hall. When we got back to the chair room, Sheppard was already there, so we thought he just got there ahead of us."

John continued to look at the table as if studying something interesting. "I kind of dozed off sitting there. I wasn't really very hungry any way."

Carson sighed, an exasperated sound. "What about breakfast?" 

John swallowed hard and tried to fight through the haze that seemed to surround his thoughts. He couldn't remember getting up this morning or going to the chair room. It was like he just was suddenly there. "I can't remember." He hated to admit that because he knew it would get him in trouble, but it scared him just enough he wasn't willing to try to cover it up.

"Then you really should eat," said Carson softly, his tone more gentle that Sheppard had expected. He made himself look up at the doctor.

"I don't know if I can eat this right now. Maybe some soup later." It was his way of telling the doctor that his stomach didn't feel like food right now and he didn't think he could force the issue. He was so tired that he ached almost everywhere, making his whole body feel "off".

Carson nodded. "All right, we'll try later. Let's get you to the infirmary."

John stood and immediately swayed, locking his knees to keep them from buckling. Ronon grabbed him before he could topple over. Once the room stopped spinning, John nodded at the big man sheepishly. "Thanks, but I'm okay now." He was grateful when Ronon eased his hand away slowly, watching to make sure Sheppard was really able to stand.

"Okay, doc, ready." John walked beside Carson as they left the mess hall. The team watched them leave and then Rodney turned to face the others. "Okay, that was scary. Did I imagine that or did Sheppard just willingly go with Carson?"

oOo

Marna helped Carson check John's vital signs while the Colonel sat on the edge of the bed, eyes periodically closing. Neither of them missed the struggle to stay awake. When they were finished, Carson tapped John on the shoulder to make sure he was aware of what he was saying. Eyelids fluttered and then opened. "Carson?"

"Colonel, you're dehydrated and exhausted. I suspect today wasn't the only time you've missed meals. I'm keeping you at least overnight so we can get some fluids into you. The scanner shows your electrolytes all out of balance as well. I'll get you some scrubs so you can change and then we'll start the IV."

John just yawned and nodded as if he didn't care. In reality, he didn't. If he could just lie down and go to sleep somewhere, he'd be happy. He was startled by hands grabbing him and opened his eyes to discover he'd been about to topple forward off the bed. Marna gripped his arms firmly.

"Uh, thanks," he mumbled, his eyes blinking slowly.

"It's all right, Colonel, just didn't want you to hurt yourself."

Carson returned with the promised scrubs and set them beside Sheppard. "Can you take care of this or do you need help?" 

John's face reddened as he sat up a little straighter. "I can dress myself."

Carson chuckled a little as he backed up a step and reached for the privacy curtain. "Just checking. Open the curtain when you're done and Marna can start the IV. How bad is the headache?"

John eased himself off the bed and leaned against it for a second. "Medium. Not nearly as bad as before. Mostly I'm just so tired."

Carson finished closing the curtain. "I'll bring you something in a moment." He turned to Marna and grinned. "Better keep an eye on him."

Marna nodded. "I'll take good care of the Colonel."

"I know that you will. Is Emira still in her office?"

"No, she went back to the lab to check the results of the last set of tests."

Carson nodded. "I'm going to check in with her and then I'll be back to make sure the Colonel is settled and get him something for the headache." Trusting Marna to take care of Sheppard's needs, Carson headed for the lab. He arrived a few minutes later to see Emira sitting on a stool and staring into space.

"Any luck with the last set?"

Emira shook her head. "No, same as the others. I think we're going to have to give up."

Carson sighed as he stood beside her, smelling the soft smell that was Emira's. He felt giddy for a moment and chastised himself for letting it get to him. "You may be right. I don't know what else to do"

Emira began cleaning her work area up. "We can do another check of the records for anything we may have missed, but barring some kind of revelation there, I'd say Colonel Sheppard will have to remain a one and only. Helia won't be happy."

Carson frowned. "We're going to have to lay down some ground rules for working in the chair then. I've just brought the Colonel in for the night. He's apparently been working six to eight hours a day for five days in the chair and he's exhausted and disoriented, as well as dehydrated. He can't even remember if he had breakfast this morning. He's not eating, something he tends to do when busy or stressed, and he's running himself into the ground. I was hoping this would work and take some of the pressure off him."

Emira thinned her lips into a grimace and shook her head. "I just don't think that's going to happen. We need to monitor him in the chair for a longer period of time to determine what's safe."

Carson nodded. "Aye, I agree. For now, I need to get back to the infirmary and see if Marna has him settled. And by now Elizabeth and the others will have come down to check on him." He turned to Emira. "Come with me and then we can get some tea."

Emira smiled up at him, her green eyes glittering. "I'd love to, but I need to clean up this mess."

"Come anyway and I'll come back here and help you after."

Emira set the dish she was holding down on the counter. "All right, I'd like that." When Carson offered his arm, she looped hers through his and they made their way back to the infirmary. They arrived to find Elizabeth, Rodney, Teyla, and Ronon waiting at the door. They stopped so Carson could talk to them.

"Is he all right?" asked Elizabeth.

"Aye, tired and dehydrated, probably from not eating or drinking much of anything over the last few days. Marna is setting him up an IV and I'll keep him overnight and maybe then some. His blood chemistry is off and we need to balance him out. Give me a minute to check on him and then you can see him. Not for long, though, he needs sleep."

Carson left them and joined Marna and Emira at John's bedside.

Marna turned to smile at him as he approached, his eyes already noting the IV had been started. "He won't be needing anything for the headache," she said.

John was dressed in scrubs and snoring lightly, his chest rising and falling with his even breaths. Carson couldn't help but smile. "That's the best thing for him right now."

TBC


	13. Chapter 13

**NOTE: **Thanks to those of you still reading. Life is CRAZY right now so I'm sorry for the lack of review responses. I love you all. I did this in kind of a hurry and late at night, so I apologize for typos and such.

The Return Part 2: Favorite Son - Chapter 13

John drifted for a while, semi-aware that he was waking, but not willing to hurry the process any. He wasn't sure what day it was or what he had to do, but for now, he was content. Eventually he opened his eyes and let them wander from the ceiling, down the wall, and across the room. His eyebrows furrowed slightly. The infirmary? He closed his eyes and tried to think, but the last few days just seemed like a foggy haze. Bringing his hand up, he rubbed his eyes, willing his mind to clear.

"Colonel, I see you're awake. How do you feel?"

John dropped his arm back to his side and looked up at Carson. "Like I've been drugged or something. Can't seem to get my mind moving forward."

Carson gave a low "Hmm," as he reached for his pen light. John moaned when he saw the offensive instrument, making Carson smile. "Now, now, Colonel, it's not that bad."

John grunted and closed his eyes for a second. "Tell me that when you're on the receiving end of that thing."

"Just hold still for me." Carson flashed the light first at the right eye and then at the left, before turning it off and pocketing it. "All done. You're reactions are a tad sluggish, but I'm not surprised at that." He slid his hand around John's wrist to take his pulse.

John waited until Carson let go of his wrist. "So, will I live?"

Carson took a long breath and let it out slowly, getting John's full attention. "Aye, but no thanks to you and Rodney. I told you not to be pulling any marathon sessions in the chair and if you began having problems, to check with me. Why do you think I tell you these things, Colonel?"

John swallowed, still trying vainly to organize his thoughts. "I, uh, I don't think we worked that hard the first day or two." John sighed and ran his hand through his hair. "Look, I don't know what to tell you. I can't . . . I don't remember much about the last few days. I don't even know how I got here or how long I've been here."

Carson nodded and looked down as he put his hand on the railing. "I was a little afraid of this. You seemed a bit disoriented when I admitted you. In a nutshell, you worked in that chair for five days straight, apparently for ten hours one those days. You were suffering from exhaustion and dehydration, so I got you to come to the infirmary with me." Carson grinned. "I knew you were in trouble when you didn't fight me on any of that."

John looked across the room without seeing any of it. He had vague images of working with Atlantis, of Rodney and Dolon giving him instructions, and a flash of being in the mess hall with the rest of the team. And he remembered being so dead tired that he didn't care what he looked like or what else was going on. He glanced down at the IV entering the back of his hand. "I'm sorry Carson. I really don't intend to . . . " John waved his hand as he lost what to say.

Carson placed a firm hand on his patient's shoulder. "I know, lad, I know. Part of me wants to throttle you and part of me . . . well, sometimes you're like a wayward child who can't seem to follow directions."

John frowned at Carson. "I'm torn between being insulted and just being glad you aren't too mad at me."

Carson shot John a warning glance. "I'd go with being glad you aren't in more trouble than you are."

John relaxed and gave a short nod. "Okay, I can go with that. How long have I been in here?"

"Since night before last. You surfaced a few times, but never completely and never for long. Sleep was what you needed, sleep and some fluids. Are you hungry?"

"Starved," said John.

"I thought so. I'll get you something light for now. You may not remember, but you haven't exactly been eating properly or regularly for several days."

John held up the hand with the IV. "I kind of figured. After I eat, can I get out of here?"

Carson paused and looked at John for several moments. "Let's get some food in you, let me check some things, and then we'll get you up and walking around. We'll see how it goes after that."

John rolled his lower lip in for a second. "So that's a no?"

Carson smiled. "Aye, Colonel, that's a no."

oOo

John was just finishing his soup when Elizabeth arrived with Rodney. "About time you woke up," commented the scientist as he approached the bed.

John tilted his head a little as he observed Rodney. "Hey, you got rid of your sling."

Rodney frowned as he looked down at his arm, still a bit red, but not nearly as bad as it had been. "Uh, yeah . . . several days ago." He glanced back up at Sheppard before looking at Elizabeth. "Did Carson say anything about brain damage?"

John sighed. "I'm not brain damaged."

"Are you sure?"

"Rodney, he's not brain damaged," said Carson, who had walked up behind them. "He's got a bit of memory loss from the time he was working in the chair, especially the last two or three days. Too much time too close together. Emira and I want to monitor the Colonel when he next sits in the chair to see if we can determine a safe amount of time and a proper break time between sessions."

"Didn't we already do that?" asked John.

"Aye, but not for a long enough period of time to see when the stress starts affecting you."

"It should be easy to monitor him any time he's in the chair, either one actually." Rodney looked surprised when all four of them looked at him.

"How is it easy?" asked Carson.

"Because the chair can monitor him and I can set you up here to receive the information. Once I make the proper connection, it's just a flip of a switch, so to speak." Rodney paused from his smug look to widen his eyes. "Did I not tell you this yet?"

Carson sighed and shook his head. "No, Rodney, you didn't. How long have you known this?"

"Oh, I thought I did." Rodney's expression sobered. "We figured it out the day we worked from the second chair. I ran across the programming and asked Dolon about it. He confirmed that it could be used to monitor whoever was operating the chair to make sure they were okay. You know, that's weird, because I could have sworn I mentioned that."

John grinned. "Okay, now who's brain damaged?"

"Funny, Colonel. Your sense of humor has _not _improved."

Carson looked at Elizabeth, his face strained. "Elizabeth . . . "

"I know, Carson. Believe me, I know."

oOo

John walked into the conference room to find Elizabeth and Helia already there. They looked up at him as he took a seat next to Elizabeth.

"Colonel Sheppard, you are looking well. I'm glad you did not suffer any lasting effects from your time working in the chair. We appreciate your help, but I wish you would not do so to the detriment of your health."

John bit his lower lip a second before responding. "Uh, don't worry about that. I don't think I'll be making that mistake again any time soon. Carson threatened to . . . uh, do unpleasant things to me the next time." He quickly averted his eyes to the table and rubbed the side of his face.

"Can I assume you've spent the last couple of days resting as ordered?" asked Elizabeth.

"Nothing but," said John.

Rodney came flying through the door, with Dolon right behind him. They carried on a conversation, arguing about the feasibility of some project and completely oblivious to the others in the room. John couldn't help flashing a grin at Elizabeth. "I think Rodney may have met his match."

Elizabeth nodded. "Kind of nice to see him get as much as he gives."

John nodded. "Makes me miss Zelenka, though."

"That's one thing we'll be discussing today," said Helia, a small smile on her face. Helia didn't seem to show her emotions easily, so any sign was a big deal.

Savill strode in to sit by Helia, with Ronon and Teyla entering to sit beside him. John felt a small pang of jealously at the easy conversation going on between the three. They had now been on several missions together while he had been working in the chair or laid up recovering from the sessions. He felt a little like he'd lost his team. _Buck up_, he told himself. _The world does not stop because you're out of commission._

"We are all here now, so we can begin," said Helia, directing everyone's attention to her.

"Uh, what about the medical corps?" asked Rodney.

Helia folded her hands in front of her. "Dr. Beckett and Emira were unable to attend, but I have spoken with them about the matters we'll be discussing."

"Oh." Rodney sat with his mouth open a little and then nodded and closed it.

"First, they have informed me that the gene therapy they've been working to develop for the two recently discovered genes will not be possible. They have exhausted all the possibilities, at least for now. Colonel, that means that you are the only known being with all three genes that is currently alive."

"Great," John muttered. He wasn't sure if he imagined it, but he thought he felt a slight tickle from Atlantis.

Helia looked at him sternly. "That means I need you to keep yourself in one piece."

John shrugged his shoulders. "I can do that. I'll just be careful."

Rodney snorted from across the room. "Sorry," he said sheepishly. "Got something in my throat."

Helia looked at Elizabeth, seeming to be at a loss for words. Elizabeth just smiled. "Yes, they're pretty much always like this. Actually, sometimes it's much worse."

"Really?" Helia's voice didn't sound like she much believed Elizabeth. "Dr. McKay, I have reviewed the scientists you have requested and information you feel supports them. I have decided to agree to the five additional people from Earth. I think their specialty areas can help us with some of the trade agreements we're working on, as well as some of the research that's needed. I'll contact General Landry this afternoon with our request."

Rodney looked pleased, but smug. "Of course, thank you. I think you'll find them a valuable asset to Atlantis."

Helia gave a small nod. "I'm sure we will. Savill, Colonel, I have a mission I need you to go on. We have an outpost on Naia that I think could be very helpful in monitoring future activities of the Asurans. We need to assess its condition and determine what it would take to make it operational again. Because of its position, it is vulnerable to attack and surveillance, so I want you to take an ample security force in case you run into trouble."

Both men nodded. John motioned toward Rodney with his head. "I assume we'll need to take a scientist or two with us on this one."

Helia nodded. "Yes, I'd advise taking both Dr. McKay and Dolon so they can complete their evaluation more quickly. And there is a chair at this site, so you should definitely go as well, Colonel."

John nodded, excitement rising within him. He'd been afraid the announcement of the gene therapy failure would come with a grounding for him so they could keep him and his connection in sight. He was relieved to know that that wasn't to be the case, at least not yet. "I'm not sure when Carson will release me for full duty. He keeps hedging when I ask."

One corner of Helia's mouth twitched almost imperceptibly as she seemed to fight a smile. "I had a talk with Dr. Beckett and Emira just a little while ago. He said if you looked all right tomorrow evening, he'd clear you for duty starting the next morning. With that in mind, I'd like to plan the mission for the day after tomorrow. Dolon, will you and Dr. McKay be ready by then?"

Dolon briefly glanced at Rodney and then looked back at Helia. "Yes, we can be ready."

"Good. Savill, you and Colonel Sheppard need to decide what security forces to take and let me know at the final briefing tomorrow evening at 1800. Colonel Sheppard, you will need to have seen Dr. Beckett by then for final clearance so we'll know if the mission is a go or not. And I believe Dr. Beckett said something about having some special instructions for you on proper chair use." Her expression remained neutral as she turned away from him to face the rest of the faces in the room. "We stand dismissed until tomorrow."

John sat a moment, contemplating what felt like his first real mission in a long time. Although he loved Atlantis, he loved going off world and exploring, seeing things most people could never even imagine. Sometimes that wasn't a good thing, but sometimes it was. And it was always exciting. As he stood, he noticed Rodney making his way awkwardly over to him, so he waited.

"Hey, McKay. Haven't seen you around the last few days. I was hoping you'd come by for a game of chess or something my last couple of days in the infirmary. Carson continues to delude himself that I can be happy lying in a bed and looking at the ceiling."

"So how did you entertain yourself?"

"Mostly by plotting my escape."

Rodney's eyes widened. "Oh my gosh, you didn't."

John frowned at Rodney like he was crazy. "No, of course not. I'm not totally nuts. I'd just get caught and end up back there with an even madder Carson and all his little torture devices. I just plotted out all the ways I could escape if I happened to lose my mind and try it. I got up one day just to walk around and stretch my legs and Carson practically had a stroke. Said I should have called a nurse in case I got dizzy or something. He threatened to give me a catheter if he caught me out of bed unsupervised again."

Rodney stood looking at John, his expression troubled. "Look, I uh, well, I wanted to apologize." His eyes drifted down to his feet.

John's smile slowly faded away. "Rodney . . . why are you apologizing? You don't usually apologize, even if you are obviously the one who screwed up. And as far as I know, you haven't done anything to apologize for."

Rodney took a deep, shuddering breath and looked up at John again. "For working you so hard and never looking up long enough to see what a state you were in. I . . . I should have noticed."

John sighed and shook his head. "No, that was my fault. I have a voice, I could have said I need a break. I'm not five, even if Elizabeth says I act like it. We both just got caught up in working on Atlantis."

Rodney sulked. "But Dolon noticed. He even tried to tell me and . . . I didn't listen. He doesn't even know you and he realized you were working yourself into a coma and I'm supposed to be your friend and teammate and I just kept –"

"Rodney! Don't get all melodramatic on me. It's okay. I'm okay. I don't expect you or anyone else to take care of me, it's not your job. You do things a certain way and it works for you. If you weren't able to shut everything out and focus you probably wouldn't have saved our lives so many times. It's who you are and I don't want you to change." He laughed and slapped Rodney lightly on the arm. "If you do our chances at survival will go down significantly."

Rodney slowly smiled. "You said almost that same thing in the mess hall when Carson figured out what we'd been doing for five days."

John looked at him blankly and then shrugged his shoulders. "I don't remember."

Rodney nodded, his face still plastered with a proud grin. "That's okay. The fact that you said it again must mean that you really believe that."

John was simultaneously grinning and frowning. "Well, duh. Why else would I say it?"

oOo

John and Savill led the way to the Ancient outpost housed in a cave in the side of a mountain. They had brought the jumper to the base of the mountain and then had to climb to the entrance. They had been going uphill for almost an hour in near tropical temperatures and they were all wiping sweat from their faces.

"Please, tell me we're almost there," complained Rodney as he walked beside Dolon.

John grinned and looked back over his shoulder. "Okay, we're almost there."

Rodney glared forward at the Colonel. "Cute. Now are we really or are you just being a jerk?"

Savill smirked as he glanced at John. "We are almost there, Dr. McKay. Just be patient."

John snorted, but didn't say anything. He felt good. The exertion and the sweat and the dirt all felt good. He grinned as he saw the cave entrance come into view. A few minutes later, they sat down around the opening to take a break. John surveyed the group. Besides the two scientists, they had brought Ronon and Teyla and three Ancients. Lino was almost as large as Ronon, but with short, blonde hair. Kasen and Kester appeared to be twins, about John's height but packing a bit more weight.

When everyone had rested and gotten a chance to get a drink, they prepared to enter the cave. John paused in front of the entrance. "Ronon, you and Kasen guard the entrance. Let us know if you see anyone or anything. Savill and I will take lead with Teyla and Lino bringing up our six. Rodney, I want you and Dolon sandwiched in the middle."

Everyone nodded their acceptance and the group headed into the cave with John and Savill leading. The cave was about eight feet wide so that they could easily walk in pairs. They moved slowly, with Savill and John carefully checking for side chambers or any sign of trouble. They had been walking twenty minutes and had long ago lost the light from the entrance, when John called a halt.

"Everyone stay put until Savill and I check this out." The two men moved forward into a large chamber, shining their lights around the rock-walled room. It was large, easily twenty five feet in diameter with a tall ceiling. The wall opposite the room entrance glistened with moisture when their lights played across it. The adjacent wall held a long, curving panel with crystal tiles, similar to the ones in Atlantis. In the center of the room sat a chair like the one in Atlantis and Antarctica. There were no other entrances or exit.

John looked at Savill to him already staring back at him. "I think we're there now."

John grinned. "Yeah, so it would appear." He stepped back and looked through the entrance. "Rodney, Dolon, you can come in now." He watched as the two scientists walked in and immediately grinned, amused by their excitement. Teyla moved in the room to stand beside him.

"Dr. McKay and Dolon seem very excited."

John nodded. "Like kids in a candy shop. Hey, how about hanging by the doorway here and keeping an eye on the part we just came through. I know Ronon and Kasen are guarding the entrance, but it doesn't hurt to keep watch."

Teyla nodded. "I agree. We have seen some odd things in the last few years."

John grinned. "You got that right."

"Okay, gene boy, get over here," called Rodney.

John dipped his head to the side for a moment, almost like he was pointing at Rodney. "His highness calls." Flashing a lop-sided grin, he walked past the chair to where Rodney stood beside the panel, unpacking his laptop.

"All I can get it to do is flicker so put your magic gene to work."

John laid his hand on the top of the console and thought _on_. The panel flickered and moaned for a few seconds before struggling to life. John straightened and stepped back a little to see if it stayed on. It did.

Rodney glanced up at the panel and nodded before looking back down at his computer. "Okay, now get in the chair."

John grimaced and walked toward the chair. "You're welcome," he murmured as he sat down. He scanned the room to find Savill making a broad sweep, Teyla and Lino watching the entrance, and Kester looking bored. Rodney continued to hook up to the console while Dolon moved over to connect to the chair control panel.

"Any time now, Colonel," came Rodney's sarcastic instructions. "We are on a time limit here."

John grinned and saluted as he leaned the chair back, feeling a connection slide into place almost as easily as in Atlantis. He closed his eyes and concentrated on finding out about the outpost. Information about the systems and their programming began automatically running through his head as he reached inside the outpost controls. His sudden intake of air caught the attention of the others in the room and all eyes turned to him as the chair shot to the upright position.

"It's booby-trapped. Savill, get everyone out, _now_. Run for the entrance and you'd better be moving fast."

Rodney and Dolon began disconnecting their computers, but John reached out and grabbed Dolon's arm. "There's no time, leave it or jerk it out and get out of here." He was relieved when both scientists just hung onto their laptops and took off, jerking the cords out and leaving them to flop on the ground. Teyla and Lino made sure the two men were out the door and came up behind them, hurrying them along.

"Colonel Sheppard, come on," shouted Savill to John as he sat back down in the chair.

"Go, I'm right behind you. I may be able to turn it off from the chair."

Savill shook his head. "No, just come on."

John waved his hand. "This outpost is important and I might be able to save it. Just make sure everyone gets out and I'll join you in a minute if this doesn't work. Go!"

John didn't wait to see what Savill did, he just leaned the chair back and began searching for a way to shut off the explosion that was building. Five minutes later, he knew it was a lost cause. The outpost was going to explode and there was nothing he could do to stop it. He leaped from the chair and took off running down the cave passage that led to the room. He knew he couldn't make it out of the cave, but he wanted to put as much distance between him and the chamber as possible. Unfortunately, time ran out quickly.

He hadn't made it very far when he heard the rumble. A split second later he was picked up by the force of the blast being funneled down the corridor and slammed against the wall. He had just enough time to realize he was screwed before feeling the flash of pain that abruptly ended all conscious thought.

TBC


	14. Chapter 14

The Return Part 2: Favorite Son - Chapter 14

Rodney groaned as the ground stopped shaking and rocks finally stopped pelting him in the back. Rubble beside him began to shift and he assumed Dolon was beginning to move around. The quaking of the ground hadn't knocked them down so much as the deluge of rocks and stones that rained down from the ceiling, along with enough dust to choke an elephant.

"Rodney, are you all right?" Rodney unfolded his arms from the protective position over his head and pushed himself up on his elbows. His shirt rode up, scratching his belly against the rough floor of the cave. He could see the light at the end of the tunnel, literally. They had made it to within sight of the cave entrance and two giant forms were barreling towards them. He hoped it was Ronon and Kasen, although all he could see was their silhouette against the outside light.

"Rodney?" Teyla's voice was more urgent this time.

"Yeah, yeah, I'm fine, if you like being buried alive in a cave in." He rubbed at a tickle on his arm and pulled his hand away bloody. Taking a closer look, he saw a gash on his left forearm. "Oh, good, I'm bleeding and in the world's most dirt filled environment."

Teyla turned to Dolon, who was now sitting up. "Dolon, are you injured?"

"No, just a little shaken up. Do you people always attract explosions like this?"

Rodney bristled. "Hey, that last one was caused by an Ancient. Come to think of it, this one may have been too since it was an Ancient outpost."

"Is everyone all right?" asked Ronon as he and Kasen barreled to a stop in front of the group sitting on the floor of the cave. Lino had helped Kester out from under his pile of rubble and they were now standing.

"I do not believe we are seriously injured, but Savill and John are farther back," said Teyla,. They all glanced back into the dark tunnel. Ronon and Kasen turned their lights on and made their way past the others, going deeper into the cave. The rest of the team got to their feet and followed. A few minutes later they came to an even larger pile of rocks, several feet deep. Near the front edge, where the debris wasn't so thick, an arm seemed to reach out from the rubble.

"Here!" cried Ronon as he began to pull stones away from the body underneath. Kasen and Lino quickly joined in, leaving little room for the others, so they stood back and waited. A short time later, Savill had been uncovered. "Teyla," called Ronon, knowing that she had the most training in field medicine.

Teyla kneeled beside Savill, checking his pulse first. Finding it relatively strong, she leaned over close to him and spoke, with one hand gently on his back. "Savill, it is Teyla. Can you hear me?" When he didn't stir, she began running her hands along his arms and legs, then his sides, looking for broken bones. She had already seen the large gash on his head.

"I'm going to try to get through to Sheppard," said Ronon, crawling over the pile of rocks.

"I'll help," said Kasen, moving right behind him. Lino didn't say anything, but silently followed the two men into the darkness.

Teyla leaned over close to Savill again. "Savill, can you hear me?" She gently rubbed his shoulder and was rewarded a few seconds later with a moan. "Just lie still. You have been injured." She studied the man's face as he slowly came to consciousness.

"Teyla?" he said softly.

Teyla smiled, relieved that he recognized her and seemed coherent. "Yes,, I am here. Can you tell me where you hurt?"

Savill closed his eyes for a moment. "Head . . . side . . . chest."

"Yes, you have a head injury, probably a concussion, and you are bleeding. I think you have some broken ribs as well. What about your neck or back?"

"No," he whispered.. "Who else is injured?"

"So far, you are the worst," she said, not wanting to mention that they hadn't yet found John. "I'm going to help you turn over, but let me know if your neck or back begin to hurt."

"Okay."

Teyla looked up at Kester. "Could you help me?"

Kester nodded and looked relieved, as if he was thankful to have something to do. He kneeled on the other side of Savill and helped Teyla turn him over. Savill grunted and held his side until they had stopped.

"Teyla?" Ronon's head appeared above the pile of rocks as he climbed partway across. "We're going to need help. It's completely blocked up here and it's taking us forever to get through."

Kester stood up quickly. "I'll run back to the jumper and call for help. Going down should be a lot faster than coming up was."

Teyla nodded. "Then go. And tell them to send a medical team as well. Savill is injured and Colonel Sheppard may be as well."

"I'm on my way." Kester turned and sprinted towards the cave entrance.

Ronon was already gone, disappearing into the dark on the other side of the rubble. Teyla looked at Rodney. "Can you help me get Savill outside? I don't know how stable the cave is and someone needs to keep watch. If this was a booby-trap, as John said, whoever set it may know their trap has been sprung and come to see what they have caught."

Rodney's eyes widened and he looked nervously back to the entrance. "You . . . you really think someone will come for us? Who? Wraith? Genii?"

"I do not know, perhaps no one. But I think it would be wise to keep watch."

"She's right," said Savill. "Help me up."

"We need to get you to sit a minute first so I can bandage your head. Then we can stand."

Rodney kneeled beside Savill and aided Teyla getting him into a sitting position. He closed his eyes tightly, obviously dizzy and in pain. Teyla took a field bandage and wrapped it around the Ancient's head, covering the cut on his forehead. Then she and Rodney each took an arm and pulled Savill to his feet. They held on tight as he swayed dizzily and almost passed out. When his legs were finally solid and the fire in his side had died down enough he could breathe, they helped him walk toward the mouth of the cave. Behind them they could hear the faint echoes of rocks being tossed aside.

oOo

Teyla looked along the path they had followed to the cave, hoping to see help arriving, even though she knew enough time had not passed. Kester had only been gone an hour and a half, not nearly enough time to have summoned help and returned. She was pretty sure Savill would recover, but she was afraid for John. Looking down, she shook Savill gently. "Savill, you cannot go to sleep."

His eyelids fluttered open as he struggled to remain awake. "Sorry," he slurred. "Did they find Sheppard?"

Teyla sighed. "Not yet."

Savill looked at her sadly. "I think he's dead. He wouldn't leave, said he was going to use the chair to disconnect . . . what ever it was that was about to explode. He stayed too long. I tried to get him to come with me, but . . ."

Teyla looked away, telling herself not to believe that. John was alive. They would find him and they would do it in time. She startled at a sound from the trees behind her and whirled around to aim her gun at the approaching noise. Ancients began to emerge from the trees, along with Carson and Emira. Teyla breathed out a long sigh of relief and lowered her gun. "I am glad you are here. Ronon, Lino, Kasen, and Rodney are all in the cave, trying to –"

She stopped when her radio activated and Rodney's voice came through. "Teyla, we found him." His voice was low and shaky, making her nervous.

"Rodney, the Ancients are here to help."

"Please tell me Carson is here because Sheppard's barely alive and I think he's hurt really bad. We're afraid to move him but we almost have him uncovered."

Carson had picked Rodney up on his radio. "I'm here Rodney and on my way with a medical team. How do I find you?"

"It's a tunnel, Carson," said Rodney sharply, the edge of fear coming through loud and clear. "Go straight and you'll run right into us."

"On my way." Carson looked at Emira, kneeling beside Savill. "I'll take a team in to get the Colonel while you tend to Savill."

Emira nodded. "Call me if you need me."

Carson motioned to several Ancients standing by with a litter and they headed into the cave. Lights came on almost immediately from the people around him as they picked their way around the debris scattered across the floor. The amount of litter increased as they moved deeper into the mountain and their progress slowed slightly.

"Carson, hurry up!" Rodney's call came from the darkness ahead, but the panic in his voice served to speed up their steps. A few seconds later, the lights from the men ahead were visible through an opening in a wall of rocks and debris stretching almost to the ceiling. As he moved to climb over the pile, he caught sight of Sheppard lying on the other side. Rodney was kneeling beside him, his fingers on the prone man's neck, checking to make sure there was still a pulse.

"I'm here, Rodney," said Carson, almost losing his balance as rocks shifted beneath his feet.

Rodney looked up and breathed out heavily. "Oh, thank God. He's barely got a pulse." Rodney stood and moved back as Carson and his medical team moved in around John. He ended up standing beside Ronon, nervously wringing his hands and trying to breathe. Feeling helpless, they watched as the medical personnel worked, calling out vital signs and wiping away some of the blood and dirt to place an oxygen mask on John's face. Several minutes later, Carson turned to the men with the litter.

"Let's get him loaded and out of here and we need to hurry. We don't have much time. He doesn't have much time."

oOo

Emira looked at Teyla, sitting on the other side of Savill. "You have done well, Teyla."

Teyla turned from watching the cave entrance to nod briefly. "Thank you. Dr. Beckett has taught me much about field medicine. He says we need it more than most of the other teams."

Emira smiled a bit as she finished putting the clean bandage on Savill's head. "I do not doubt that."

Savill winced as Emira completed her task. "She did a good job of keeping me awake. Wouldn't even let me get in two seconds of rest." He smiled at Teyla, reaching out to grip her arm firmly. "They'll get Sheppard out. Your Dr. Beckett seems like a very skilled healer."

Teyla nodded. "He is. And he has saved us on more than one occasion. I'm just concerned that there will come a time that there is nothing that can be done. Colonel Sheppard is . . . a very close friend. We have all come to rely on him in many ways."

"I understand," said Savill softly, his tone comforting and warm. Savill looked up at the man standing in front of him. "Tavey, how did you get here so fast?"

The short man with dark hair smiled nervously as he squatted in front of Savill. "Sir, we knew from Kester that we needed to hurry, so we tried to find a closer place to set the jumper down. There's a small clearing just above this position, so we set down there and came down to you. It's a tight fit, but it shaved a lot off our response time."

Savill started to nod, but stopped abruptly and winced. "Good work. Anything new on Sheppard?"

"They're on their way out now," said one of the other Ancients, his hand on his radio.

Teyla stood and turned to watch the cave. Emira also stood. "Let's get Savill up and start toward the jumper. He'll probably need help and he may not be able to move quickly." Two of the men moved forward, carrying another litter.

"Oh, no you don't," Savill said softly, but firmly. "I can walk. Help me up."

Tavey took his arm and helped him to his feet, holding on when he swayed. Teyla couldn't help but smile, thinking about how much he was starting to remind her of her own team leader. Definitely stubborn.

Savill narrowed his eyes, which didn't look entirely focused. "What?"

Teyla just shook her head once. "Nothing."

Savill snorted and then quickly put his hand to the side of his head. "Dumb," he muttered under his breath. "Someone show me where this close jumper is." Emira and Tavey got on either side of him and they began going back the way the Ancients had come in. Teyla waited on the group carrying Sheppard.

Several minutes later, four Ancients emerged carrying the litter with John. She couldn't see his face for the oxygen mask and the bloody bandages wrapped loosely around his head. She stood in front of the cave as they carried him past her, Carson and one of the nurses close behind and watching. Rodney, Ronon, and the others came out a few seconds later. She fell in step beside her teammates.

"How is John?" Fear gripped her because of the grim look that had been on Carson's face.

"Not good," said Rodney. "Not good at all. The only thing Carson's really said so far is that we need to hurry."

Teyla glanced at the path before them. That didn't sound good at all. They had walked for several minutes when she felt it. She stopped suddenly and stared at the area around them, her hand holding tightly to the P90.

"Teyla?" said Ronon hesitantly.

"Wraith," she said firmly as she looked toward the sky.

Rodney's mouth dropped open and his eyebrows shot upward. "Wraith? Oh, no," he squealed. Kalen and Lino stared openly at Teyla, then looked to the others in confusion. Their confusion grew when two Wraith darts raced by overhead.

"Holy crap! We've got to get to the jumper. We can cloak it and they won't know we're here, right?" Rodney's voice had crept upward in pitch as his panic increased.

"I think they already know we're here," said Ronon as they all picked up speed and began jogging through the woods. "They're probably the ones that set the outpost to explode."

"Oh, no," mumbled Rodney again, already beginning to pant.

Ronon paused when the whine of a drone flying overhead became incredibly loud, indicating the ship was flying low. It barely cleared the tops of the trees as it passed overhead. Ronon quickly sighted and shot, the red pulse of energy hitting the ship just before it flew out of sight. They heard the engines falter, followed by a brief explosion. Ronon flashed Rodney and Teyla a feral grin.

"Ronon," Teyla hissed. "You have just given away our position. That was not wise."

Ronon smirked. "Maybe not, but it sure felt good. That's one down for Sheppard, and if they're the ones that set us up, it wasn't enough."

The sound of weapons fire from behind them stepped up the urgency of the situation. Teyla's scowl deepened. "They are on the ground and moving in. We must hurry." She turned to run the way the others had gone. Ronon and Rodney glanced briefly at one another and then fell in behind her, their steps increasing as the fight behind them drew closer.

They broke through the edge of the forest into a small clearing. Rodney's first thought was that they had come to the wrong place. The clearing seemed to be too small for the two jumpers that had come and it was empty. At least it appeared that way until Carson seemed to vanish in thin air. Before he could say anything, he realized the jumpers were cloaked. One of the Ancients leaned out the back hatch to direct them to the right place. Darts whined overhead, adding a little motivation.

Rodney figured the pilots must be really good to even have attempted the landing in that tight a space. Sheppard was the only one he would have trusted to try such a maneuver. Of course the Ancients had had a few more years to practice than most of the Earth pilots. They entered the back of the jumper to find Carson and Emira working over John again, checking vitals. Carson had John's shirt up, pressing around the Colonel's abdomen and doing his doctor thing. John's shirt was in tatters and he was covered in scrapes and bruises. His ribcage seemed malformed and Rodney had to look away as his last meal tried to make a reappearance.

Lion and Kasen rushed into the jumper and the hatch began to close. Rodney looked around almost in a panic. "Wait, that's not everyone is it?"

Savill, who was sitting across from him, gave a small, appreciative smile. "They will return in the other jumper. We need to get Sheppard back to Atlantis."

Rodney looked back down at John. "Oh . . . yeah. What about the gate? Are the Wraith keeping it active to block us?"

The Ancient sitting next to Savill shook his head. "No, they didn't come through the gate."

Rodney's face got even whiter. "There's a hive ship nearby?"

"It's okay, Dr. McKay. We won't be here long," said Savill.

"What . . . what about the other jumper? And Kester?"

"Kester took the jumper you came in back to Atlantis after we arrived," explained the mystery Ancient. "He was too far away to help and there wasn't room in the clearing to put another jumper, so we sent him back to inform Captain Helia of exactly what happened."

He watched in morbid fascination as Carson and Emira checked Sheppard's condition manually, as well as with the monitor they had connected. He was a little amazed at the Ancient technology. It seemed to have everything covered and yet it was actually smaller than the heart monitors from Earth.

A few minutes later, the pilot informed them they were approaching the gate and he was beginning the dialing sequence. Rodney finally began to relax. He knew Sheppard's chances increased if they could just get him back to Atlantis and they were almost there. He could see the shimmering puddle of the event horizon getting larger as they closed in and he allowed himself a small sigh of relief.

Just before they entered the wormhole to Atlantis, Carson announced that Sheppard had stopped breathing. The alarm for the heart monitor began blaring as they passed through the gate. Rodney's last thought before being demolecularized was that Sheppard's luck had finally run out.

TBC

_I know, two in a row isn't fair. And who told you life was fair, because they were seriously wrong. _


	15. Chapter 15

The Return Part 2: Favorite Son - Chapter 15

As soon as the jumper passed through the gate and into Atlantis, Carson and Emira were in motion. Carson intubated John in almost the same way as usual. Rodney noticed the instrument he used looked slightly different, but seemed to operate about the same way. The unusual part was that it was then hooked up to the machine that was monitoring the pilot and began pumping oxygen into John with the push of a button. Apparently the monitor also served as a portable ventilator.

When Carson had finished, Emira called, "Stand clear." As Carson leaned away from John, she pushed another button, sending the Colonel arching off the floor. The monitor pads also acted as a defibrillator. Rodney was amazed at how quickly the events unfolded before him. Unfortunately, the alarm was still blaring and the monitor screen wasn't showing anything that looked like a heartbeat.

"Stand clear again," said Emira before pushing the button one more time. Rodney couldn't help but remember the time this same scene had played out in the jumper after the iratus bug had been removed from the Colonel's neck. Rodney swallowed hard and clasped his hands together, hoping the end result would be the same. He had barely known Sheppard then, and yet he had silently urged the man's heart to start beating and found himself terrified it wouldn't. He was even more afraid now. Atlantis wouldn't be the same without Sheppard. _He_ wouldn't be the same without Sheppard.

The rhythmic sound filled the silence of the jumper and he heard an audible sigh of relief from Carson. "Sinus rhythm. We got him back."

The jumper had landed in the jumper bay by then and the back hatch was dropping to reveal medical personnel standing by. The ramp barely hit the floor before they rushed in with a gurney and carefully loaded Sheppard onto it, then rushed back out, Carson running along side the stretcher. Emira waved in the next stretcher and began helping Savill to stand.

"I can walk, I don't need a stretcher." His knees buckled as soon as he was upright and Ronon jumped up to help catch him when he pitched forward. Ronon soon realized the Ancient, limp in his arms, was unconscious and he lifted him up and laid him gently on the gurney. Emira did a quick check of the man before sending the stretcher to the infirmary. "Walk to infirmary indeed," she muttered as she turned to the others.

Rodney noticed that everyone but him was standing. Teyla leaned over to take him by the arm and he allowed her to help him stand, but he wasn't sure why. He wasn't injured badly, but he felt numb and out of touch, like he might just float away if he wasn't anchored down.

"Dr. McKay, you're bleeding."

Rodney looked blankly at Emira for a few seconds before looking down to see spots of blood soaking through the bandage on his arm. "Oh . . . yeah . . . I guess I am." Now that he was looking at the injured appendage, he began noticing the burn of the cut beneath the red and white gauze. He looked back up at Emira. "Sheppard . . . he's gonna be okay, right?"

Emira pursed her lips a second before putting on a small, strained smile. "I'm sure Carson will do everything possible. I really need to get back to the infirmary in case he needs help. Can everyone else make it on their own?" When everyone left in the jumper nodded, she gave a curt nod and hurried down the ramp.

Rodney felt a small tug when he tried to move forward and realized Teyla still had hold of his good arm. She recovered quickly and fell in step beside him. "I'm sorry, I did not realize you were ready," she explained.

"I can make it okay," Rodney said softly.

Teyla looked at him, her eyes wide and as full of fear as he'd ever seen them. "I know," she said quietly, tightening her grip slightly. Rodney just nodded and continued the long journey to the infirmary.

oOo

Elizabeth met Ronon, Teyla, and Rodney in the hall on the way to the infirmary. "Are any of you hurt?" she asked as her eyes raced over each of them.

"Not seriously," said Teyla. "Rodney has a large cut on his arm and we are bruised from the falling rock. Savill has a more serious head injury and John . . ."

Elizabeth paled and almost stopped. "What about John?"

"It's pretty bad," said Ronon, his voice quiet and low. "He was buried in the rubble for a while before we got to him. His heart stopped just as we got to Atlantis."

Elizabeth did come to a stop this time, her eyes wide. "He isn't . . ."

Rodney shook his head. "No, Carson and Emira got him back, but he's hurt really badly. I think he's got some broken ribs, at least it looked like it when Carson was examining him in the cave. His side was a mess and . . . I think maybe he's got a bad head injury too. There was an awful lot of blood and Carson wasn't happy when he did his penlight thing."

Elizabeth let out a deep breath and closed her eyes for a few seconds. "Okay." She started walking toward the infirmary again, her heart beating fast in her chest. A few minutes later, they entered the medical facility of Atlantis to a bustle of activity. Savill was being treated by some Ancient personnel they were unfamiliar with. Carson and Emira were working over Sheppard with a couple of nurses. They stood near the door, staying well back out of the way while watching the frantic motions around the Colonel's bed. Suddenly the doctors stepped back and the bed was wheeled through some doors with Carson close behind it. Emira turned and looked around for a second until she made eye contact with the group at the door. She arrived at the group about the same time Helia joined them.

Helia walked up to stand beside Elizabeth. "I'm sorry for the delay. I was making sure everyone made it back to Atlantis."

Elizabeth nodded. "Is everyone safe?"

"Yes, the last jumper just made it back. I'm afraid we lost two men in the ground attack and there are a few more injuries, but most of them seem to be minor. How are Savill and Colonel Sheppard?"

Emira nodded toward where Savill was being treated. "Savill has a severe concussion. We'll have to monitor him for a day or two to make sure nothing more serious develops, but I think he'll be okay."

"That is good news," said Helia.

Emira nodded again and looked down at her data pad for a few seconds. "Colonel Sheppard was injured more seriously. He has a skull fracture, so we'll have to keep a close eye on him for swelling or bleeding in the brain. The more immediate danger is internal bleeding. He has several broken ribs and a few more cracked ones, and I'm afraid they've done a bit of damage internally. He's bleeding quite heavily and Carson is taking him to surgery. I'll be scrubbing to help as soon as we're done here. The Colonel also has some smaller injuries like a broken collarbone and dislocated shoulder, but the internal bleeding is our first priority. I need to go, but we'll let you know as soon as we're out of surgery." Emira turned and hurried through the doors Carson and the gurney with Sheppard had gone through earlier.

They stood in silence for a few minutes before Rodney sighed and scratched his head. "I hate this." He stared at the doors across the room. "Sometimes I hate him."

Teyla came up to stand beside him. "You do not mean that."

Rodney snorted and walked forward a few steps only to stop and pace back the way he came. "Yes, I do. Stupid hero complex of his. That stupid mindset that he's expendable and should send everyone away while he fiddles with the chair until the last second. Why didn't he just run with the rest of us? We'd all be sitting here with bumps and bruises and complaining about all the dust."

"You heard Savill. Sheppard thought he could turn the thing off and save the outpost. He had to try, McKay. You know he couldn't walk away if there was a chance of saving the outpost and all of us." Ronon crossed his arms defiantly, a deep scowl on his face. They weren't sure if he was angry with McKay or just angry with the circumstances.

Helia tilted her head slightly and frowned. "Wait. We know you found the outpost and that is was a trap, set to explode shortly after you activated it. We also know it exploded with some of you still inside the cave, but that is all. What happened?"

Teyla brought her head up and took a deep breath. "John knew shortly after he sat in the chair and told us to get out, that the outpost was . . . booby-trapped. I heard Savill encouraging him to come with us as we ran through the tunnel. We were almost to the entrance when the explosion occurred. When we went back, we found Savill, injured. He said that the Colonel thought he could use the chair to stop the explosion, so he stayed behind."

"Yeah, well, we see how well that worked," mumbled Rodney, balling his hand into a fist and smacking it soundly against the wall behind him.

Helia gave a slight nod to Teyla. "Thank you, I will talk to Savill when he is able. Dr. McKay, it appears you need to be treated. Your arm is bleeding." She turned to one of the nurses passing by. "Someone needs to look at Dr. McKay's arm. He is injured." The woman nodded and motioned for McKay to follow her. Rodney didn't move until Teyla placed her hand on his back and pushed him forward a step. Reluctantly, he made himself move forward and follow the petite woman across the room after taking one last glance at the doors that separated them from their friend.

oOo

Rodney sat on the edge of the bed, his arm neatly cleaned and bandaged. They had waited for hours. Once all their injuries had been treated, the Ancients had insisted they leave the infirmary to make room for the new injured being brought in from the other jumpers. Helia had been able to have a brief conversation with Savill before going back to the control room. John's team had stood in the corridor and watched as people were released and left one by one. Slowly, but surely, they had crept closer and closer until they were back inside the doors.

They were noticed a short time later and asked to wait in the hall again. Apparently the Ancients had stricter rules about hanging around the infirmary waiting to hear about your teammate's condition. The nurses gradually became more sympathetic to the group of humans that kept peering around the corner and trying to gleam information. They were allowed to come in and sit around to wait for word on Sheppard as long as they didn't disturb the few other patients currently confined.

"Dr. Weir?"

They all looked up at the nurse standing in front of them. "Yes?" asked Elizabeth, her voice edged with worry.

The nurse smiled. "Colonel Sheppard is out of surgery. Dr. Beckett will be with you in just a few minutes. He's getting the Colonel settled in recovery."

Elizabeth breathed out a long breath. "Thank you." She looked around at the others and saw the relief on their faces as well. They all focused on the door, waiting on Carson's form to come through. It was a few minutes that stretched on like forever before the doctor came out to talk to them. His face was tired and grim.

"I guess Crenia told you we were out of surgery. It was close, I'll tell you that. The Colonel lost quite a bit of blood and his insides were a mess. That along with the delay in getting medical attention . . . let's just say it's a testament to how stubborn he is that he's still alive."

"He's going to be okay, though, right?" asked Rodney.

Carson hesitated and looked down. "I don't know Rodney."

Rodney's eyes widened and then his brow furrowed in a deep scowl. "What do you mean you don't know? What kind of doctor are you? Is he going to live or not?"

"Rodney," Carson said softly. "The Colonel is in very critical condition. Between the blood loss, the shock, and the head injury, he's barely holding his own. We nearly lost him twice on the table. We'll just have to wait and see. If he can hold on the next couple of days, his chances get better."

"Can we see him?" asked Elizabeth.

Carson sighed and nodded. "In a bit. Wait until we get him settled in the critical care area and then you can take a peek. It will have to be a quick in and out. He'll be monitored constantly with medical personnel coming and going. We need ready access to him and I won't compromise on that. I should warn you he's on a ventilator. In all that moving, one of his ribs punctured a lung and he's not breathing on his own. Just sit tight and I'll come get you when we're ready." Carson turned partway around before moving back to face them. "I can promise you that we'll do everything we can. You just need to know . . . it may not be enough." He moved quickly back through the doors, leaving them to think about his statement.

oOo

Rodney lay in his bed, staring into the dark. He'd been there for over an hour, just staring at the ceiling in the shaft of moonlight streaming through the window. Carson hadn't sounded very confident that Sheppard would survive. And since seeing the man, neither was he.

Sheppard was a mess, his face unnaturally pale, probably from the blood loss. A large bandage had covered most of his head and there had been tubes and wires, fluids and monitors. The ventilator had been the most unnerving of everything, the evidence that Sheppard would be dead very quickly if it stopped for any reason. He was too weak, too injured to even breathe for himself. No matter how many times Rodney told himself not to think about it, that Sheppard would be Sheppard and survive, the doubt kept edging in and making his gut churn with fear. He closed his eyes and tried to make himself relax so he could get some sleep. He had a feeling the next few days might be long ones.

oOo

Carson looked at the group assembled in the conference room. Emira sat beside him and then Helia beside her. Moving around the table sat Elizabeth, Teyla, Ronon, and Rodney. It was almost evening and it had been a long and frightening twenty-four hours. He thought it just might be about to get worse.

"I wanted to give you the latest on Colonel Sheppard's condition. I'm afraid it isn't good. There is swelling in the brain, which is increasing slowly at present, but if it continues, may become a serious problem. He still isn't breathing on his own and his blood pressure is slowly dropping."

Rodney's voice was high pitched and nervous. "What are you saying?"

"His condition is deteriorating instead of improving."

"Carson?" Elizabeth was sitting ramrod straight, her features drawn tight with exhaustion and worry. It was apparent none of the members of John's team had slept.

Carson looked around at each of them. "Emira and I are afraid the Colonel will not recover if we allow things to progress as they are. She has an idea that might increase his chances."

"What is it?" asked Ronon.

Emira looked at each of the faces in front of her. "We have a medical pod that can be used to treat critically ill patients like the Colonel. It will lower his metabolic rate and systems, similar to a stasis pod, but not as deep. It provides total support for the body, including intravenous fluids and medications. It monitors everything, including brain waves and blood chemistry and is able to detect even the slightest fluctuation and adjust treatment accordingly. Because of the level of support and the slowed bodily functions, we have found the chances of recovery to be greatly enhanced."

Teyla glanced at the others and then back to Emira. "Do you feel this is John's best chance?"

Emira nodded. "Yes, I do. It is not a fast process, but we have had great success with it."

Rodney frowned. "What do you mean by not fast?"

Carson let out a huff of air. "From the level of the Colonel's injuries and his current condition, he would probably be in the pod for three to six weeks."

"Six weeks?" said Rodney. "That's too long. If you don't put him in that thing, he'll be back on his feet and running with Ronon in that length of time."

Emira looked at Rodney, waiting until he made eye contact with her. "Dr. McKay, you are correct in that if the Colonel can recover on his own, it would occur faster than by doing so in the pod, although you may have exaggerated to what extent. But we have found that even though the pod slows the recovery, it increases the survival rate and provides for a much more complete recovery. Patients that otherwise might have permanent effects from injuries were able to heal completely with this method. I believe it is the best course of action for Colonel Sheppard. I believe it is his best chance of survival."

They sat in silence for several minutes, letting the information sink in and dealing with the possibility that Sheppard might not survive. Elizabeth finally looked at Carson. "What do _you_ think?"

"I've studied the information about the pods and the history of its use in treating severe injuries like the Colonel's. I also think it's the Colonel's best bet for living through this. His chances without something extreme like this are very slim."

Helia looked at Elizabeth. "This is your call. Colonel Sheppard is your friend and I feel you best know what his wishes would be."

Elizabeth looked at Ronon, Teyla, and Rodney, each of them giving a short nod in turn. She smiled, small and bitter, and turned back to Carson. "Do it."

Carson nodded. "I believe this to be the right decision."

Rodney raised one hand. "Can . . . we see him . . . you know . . . before . . ."

Carson looked at Emira, who nodded. "Give us an hour to get it set up," she said.

oOo

Rodney led the group into the infirmary, where Carson stood waiting for them. "We're about ready. Follow me." He led them through a door, down a hall, and to a room in the back. Rodney was pretty sure he'd never been to this room before. A pod extended out from the wall, the top half open to reveal Sheppard inside.

Rodney stared. "Like the _Aurora_," he whispered.

Helia was already there and she jerked her head up to look at the scientist. "The _Aurora_? What do you know of the _Aurora_?"

Rodney let out a breath and looked down. "I know the crew is dead, the ship destroyed. They died taking out a Wraith ship."

Helia looked sad, but not surprised. "Will you tell me about it later?"

Rodney nodded. "Yeah. I think you'll be proud of them. But this," he waved his hand toward the pod. "This reminded me of the pods the crew was in."

Emira nodded. "They are similar, but for a different function."

The team made a semicircle around the pod with Sheppard. A sheet covered him from the waist down, but his visible torso was bare except for the bandages. They could see parts of a few tubes and wires connecting him to the inside of the pod. Even the ventilator tube was connected to a port inside the pod.

"What about the brain swelling thing?" asked Rodney.

"The pod will monitor intracranial pressure as well. If any conditions arise that the pod is not equipped to handle, an alarm will sound and the monitor will tell us exactly what the problem is. We'll have someone keeping tabs on the Colonel at all times in case there are any problems." Emira took a step closer to Rodney and put her hand on his, waiting until he looked at her. "I promise, we'll take good care of him."

"Six weeks?" he asked sadly.

"It may not take that long," she responded.

"May we come see him?" asked Teyla. "Talk to him, so that he knows we are here."

Emira frowned for a moment before her features returned to a neutral expression. "Colonel Sheppard will not be able to hear you, but we may be able to work out some brief visits on a weekly basis."

Teyla looked at Carson as if confused. Carson smiled. "That, lass, is one point where Emira and I do not necessarily see eye to eye."

The nurse working at the pod turned to Emira. "We're finished. Colonel Sheppard is ready."

Emira nodded at the woman. "Thank you." She turned back to the team. "You have time for a quick good bye before we activate the pod."

Teyla moved toward John and leaned over, stroking his cheek. "Get better, John. We will be waiting when you emerge." She leaned over to touch her forehead gently to the bandages covering his. Standing, she walked away.

Ronon came up beside John and looked down at his unconscious and too still form. "You better not die on me Sheppard. Not after everything we've been through. If you do, I'm kicking your butt."

Rodney rolled his eyes and replaced Ronon beside the pod. "Don't listen to him. He can't help being a barbarian. Look, Radek is coming to Atlantis in a few days. You can't just abandon me with him. So just get your lazy self to healing and get out of this thing soon. I can't come after you like I did on the _Aurora_." Rodney shifted his feet nervously and then walked over to stand beside Teyla.

Elizabeth knelt beside the pod and placed her hand on John's arm. "We're here for you John, just remember that. There are people here that care for you very much. You fight like I know you can fight and we'll be waiting for you when you get better. Just let Atlantis take care of you." She hesitated and then leaned over, placing a light kiss on his cheek. "We'll miss you in the meantime," she whispered in his ear.

Rodney was gaping at her as she walked past him. "Close your mouth, Rodney, you'll catch flies. And don't make more out of this than it is."

Emira nodded to the man at the control panel next to the wall. He pushed a tile and the pod began to close and slid a little further into the wall, where only the top half of Sheppard's torso was visible through the clear shell. They all stood looking, unsure of what to do next, until Carson finally spoke up.

"It's time to leave. I'll be keeping watch over him. I'll let you know how he progresses." He moved toward the door and it slid open, allowing Sheppard's team to file out one by one. The sound of the door closing behind them seemed ominous, making Elizabeth shudder.

oOo

John felt lost. One moment there way pain, unending and agonizing pain. Voices and touches and then quiet and blackness. The pain and the voices came and went in a flurry of confusion that kept his mind spinning dizzily. The agony seemed to go on forever and if he was capable of a conscious thought, it was for the misery to end.

And then it changed. Suddenly he was wrapped in soft warmth, almost like a living embrace. The pain was there, but muted and pushed back. Silence prevailed, but it was not a cold, harsh silence. It was a comforting silence. John relaxed into whatever was happening, feeling that he could accept the outcome, whatever it was. He felt like he was home.

TBC


	16. Chapter 16

The Return Part 2: Favorite Son - Chapter 16

They drove Carson crazy for the first five days. Each and every day, the team came by at least once to see if they could sit with Sheppard. Each and every day, Carson explained why that was not allowed. They may have picked up on the lack of conviction behind the argument, because the next day they would show up again and listen to the same lecture. On day five, Rodney called Carson on it.

They stood quietly while the doctor told them that they would be in the way and the Ancients didn't allow that sort of thing and that Sheppard was out like a light and wouldn't know they were there anyway.

"Bullcrap! Do you have any idea how hypocritical this makes you?" asked Rodney, his arms crossed defensively and a scowl on his face. "You always let us sit with him before, even encouraged it in times like this. You said you thought people in comas had some level of awareness, even if it wasn't conscious. You said he might recognize that people he cared about were with him, that he wasn't alone. I even heard you tell Elizabeth that sometimes you thought that was the only reason we survived some of the things we've been through. You can't tell me that you suddenly think it makes no difference."

Carson sighed and looked down, defeat in his face and posture. "I still believe that," he said quietly.

Teyla frowned and stepped forward, putting her hand gently on the doctor's arm. "He is alone, Carson. Why may we not stay with him then, and comfort him when he is in pain?"

Carson looked from Teyla to Rodney to Ronon. "Because, whether we like it or not, this is Atlantis, the city of the Ancients. They built it and it is rightfully theirs. I must abide by their wishes and their rules, even if I sometimes don't agree. The Colonel is still alive and he is doing as well as can be expected. If it weren't for the Ancients and that pod . . . I honestly think the Colonel would be dead by now. We can show our gratitude by respecting their wishes, even if it's a bit hard to take."

It was quiet for a few moments. There was no way to argue with Carson's words, even if they wanted to. Teyla finally gave a small nod. "We understand. May we still see him at the end of the week."

Carson nodded. "Aye, Emira promised us that. Just be patient."

Rodney snorted. "You know I'm not good at that."

"Aye, we all know that," said Carson. "Look, you can still check with me whenever you want, but unless Emira changes her mind, you can only see him once a week. That's the way it has to be. I can assure you that we are keeping a close watch on him and that he's receiving the best care." Carson smiled. "And I make sure I speak to him every day, tell him how annoying you've been."

Ronon cracked a small smile. "Tell him to hurry up and get better. I need a running partner."

Teyla grinned. "And I a sparring partner."

Rodney nodded. "Yes, yes, and I need a . . . a . . . someone I can insult."

Carson chuckled. "I thought Radek was coming tomorrow."

"Oh, yeah, I forgot. Well, I can't exactly use my Kirk or flyboy insults on him, now can I?"

Carson grinned as he patted on the shoulder. "No, I guess you can't. I'll be sure and deliver the messages."

oOo

Rodney had mixed emotions as the new scientists came through the gate, Radek in the lead. He was really glad to see Radek, but an empty place existed as well. He swallowed and stepped forward to meet the new arrivals, ignoring Helia and Elizabeth in the background talking to General Landry at the SGC.

"Radek, you old goat, you're back."

Radek set his heavy bag down on the gateroom floor. "Yes, I am back. I almost not come when they tell me I have to work for you, but Atlantis, well, she is worth the sacrifice."

"Hah! It's me doing you the favor by taking your worthless, paranoid self in. I almost couldn't convince them to let you come back."

Radek sighed. "Rodney, you always were bad liar." He looked around the room, let out a deep sigh, and smiled. "It is good to be home, yes?"

Rodney nodded. "Yes."

"How is Colonel Sheppard? We heard he was injured."

Rodney's smile faded and he looked at the floor, the empty place once again gnawing at his gut. "He's not doing so well. Carson and Emira, one of the Ancient doctors, have him in some kind of medical pod. I just hope it works."

Radek looked long at his friend. "Colonel Sheppard is strong man. He will not give up."

"I know. Come on, let's get you settled so you can start nagging me like an old ex-wife."

Radek picked up his back and snorted. "As if anyone would marry you in first place. It is you who are nag." The two men started walking across the room.

"Rodney?" Rodney stopped to look up at Elizabeth, standing at the railing with a smug grin. "Aren't you forgetting something?" She gave a short nod toward the opposite end of the room.

Rodney turned to see the other four scientists looking confused. He sighed and shook his head. "All right, children, pick up your bags and follow me." He gave a short nod to Elizabeth. "Happy?"

"Very," she replied lightly.

oOo

At the one week mark, Rodney, Ronon, Teyla, and Elizabeth were waiting in the infirmary for the promised visit. Ten minutes after the appointed time, Carson finally emerged from the bowels of the medical wing.

"It's about time," complained Rodney. "You guys make us wait a week and then you're late. What kind of joint are you running here? So, lead the way."

Carson hesitated for a moment before speaking. "I'm sorry, Rodney, it couldn't be helped. We've had a wee bit of a problem with the Colonel the last few hours. I'm afraid the intracranial pressure rose to dangerous levels during the night. I think we have it regulated now, but it was touch and go for a bit. All right, come with me."

They followed Carson to the back room with the medical pod and nervously entered the room. Rodney led the way to the pod, anxious to look in and see that Sheppard was still there. He was and he didn't look much different than the last time he saw him except for one thing. A small area of hair at the edge of his temples had been shaved back slightly to accommodate a metal rod that extended from the inside of the pod to his head. Rodney leaned over to get a closer look.

"Carson, what is this?"

Carson glanced down, but he already knew what Rodney was talking about. "We had to relieve the pressure before it resulted in brain damage. Those monitor the exact pressure and open to release some of it when needed. It's a lot more accurate and quick to respond than what I'm used to."

"But . . . but he has metal bars in his head," Rodney sputtered. "How can that be good?"

"They aren't bars. It's a very sophisticated array of sensors and release valves. It's doing the trick, Rodney, that's all you need to know."

Rodney frowned and turned back to Carson. "It's bad enough we put him in there, but now . . . it's starting to look more like a torture chamber."

Carson's face reddened slightly as he began to lose his patience. "He can't feel any of it and it's keeping him alive. What do you want me to do, let him die? Because that's the alternative."

"No, of course not, I just . . . I . . . " Rodney turned away and walked over to face the wall. Carson sighed and rolled his eyes, walking over to stand behind the scientist.

"I won't do anything I think will hurt him. He's my friend too."

Rodney continued to stare at the wall. "I know. I just wish this didn't have to happen. I wish we could do something for him."

"We are, Rodney," Carson said quietly. He turned to the rest of the team. "You have fifteen minutes." He slipped out of the room, almost unnoticed.

Teyla walked over to stand by the pod, putting her hand on top of the hard, clear top. After a moment, she moved her hand down to the side, where it could rest beside John's hand on the other side of the glass. Rodney could see the lack of touch was really getting to her.

"We have missed you John. I hope you know that you are not alone. We will come to you as often as they will let us. I am sorry we must leave you alone so much of the time, but you are constantly in our thoughts." She rubbed her hand along the glass, barely an inch from Sheppard's arm.

Rodney walked over to stand behind her. He was proud of himself for not voicing the thought foremost on his mind, which was that Sheppard looked like a corpse lying in a coffin. He shivered when he imagined being locked in that tight space, especially for over a month. He couldn't do it, at least not if he was conscious.

"Radek is here. He asked about you, said to tell you to keep on fighting. Actually, he said if you didn't get better soon so I'll have someone else to insult, he's going to come yank you out of there himself."

Ronon frowned. "He's only been here one or two days."

Rodney nodded. "He's a whimp. He always was."

Ronon grunted.

"What's that supposed to mean?" asked Rodney indignantly.

"Nothing. Just seemed like the time it takes for you to drive people crazy has gotten shorter. You've been practicing."

Rodney leaned over the pod, placing his hand palm down and moving his face to within an inch from the surface. "Sheppard, I swear, if you don't get better and get out of there soon, we're going to have problems here."

"Oh for heaven's sake," muttered Elizabeth, shaking her head. "I'm beginning to understand why they only let us in here once a week. Carson's afraid John will decide to just stay in there as an escape."

The banter continued for a few more minutes, but died down as time drew short. The attempt to lighten the mood couldn't hold up when put up against the knowledge it might be another week before they could see the Colonel. The mood quickly turned somber and silent.

Carson came in a few minutes later to find them surrounding the pod, staring down at their friend, their hands on the top of the pod. He waited for a minute before joining them and adding his hands to the surface.

Elizabeth eventually looked up at Carson. "Do we really have to wait a week?"

Carson sighed. "I'll talk to Emira. I think we can work something out."

oOo

He floated in and out of pain, but the warm presence was always there. Fire raced through his head, obliterating thoughts and awareness of anything else, but then comfort surrounded him and the pain became bearable. Voices soothed his aloneness and warded off the feelings of abandonment. There were no organized thoughts, just random feelings and sensations. But she was always there, and for that, he was grateful.

TBC


	17. Chapter 17

The Return Part 2: Favorite Son - Chapter 17

Emira looked across her desk at Carson. "I just do not understand why they want more time with Colonel Sheppard. He cannot hear them. He will not know there are there and their presence will not improve his condition. The visits serve no useful purpose."

Carson sighed and rubbed the side of his face, trying to figure out how to explain the connection that existed between the members of the team. "I get the impression that we are . . . more emotional that you and your people. We form deeper attachments to our friends, our teammates. This is as much for them as for the Colonel. They have a need to see him, to know that he is still alive and that he has a chance. As for it helping him, I also happen to believe that unconscious patients may have some awareness of what's going on around them. They may hear voices and feel touches on some level that lets them know they are not alone. There is evidence to suggest this is more than a passing thought."

Emira took a deep breath and let it out slowly, thinking as she sat. "I still do not entirely understand, as we would most certainly let Colonel Sheppard's friends know of any change in his condition, but I will accept your word on this." She paused a few seconds and then the tension in her face relaxed a little. "I suppose it would not hurt for them to visit the Colonel more often, if they are willing to make it short and keep out of the way. They could visit each afternoon for a few minutes."

Carson smiled and nodded, relief evident in his expression. "That would be fine, Emira, and thank you. I'll be sure to meet them each day and oversee their visit, so it doesn't interfere with the duties of your staff. I'm sure they'll be grateful. I know you don't think this is necessary, but this will ease their minds a lot."

Emira nodded and gave a small smile. "I am glad we were able to work something out." She chuckled a little. "I may not understand your people, but I have become rather fond of them. It has been interesting to learn of the things we have in common and the things that are different."

"Aye, that it has. And I'm grateful for the opportunity to learn about some of this technology."

"You are a fine healer and a quick learner. It has been an honor to work with you as well. I have noticed that you are very close to the others."

Carson smiled and leaned forward in his chair, resting his arms on his thighs. "Aye, I'd say we've become good friends over the years."

"Is that wise? Does it not impede your ability to treat them when they are seriously injured?"

Carson looked down sadly. "Mostly it makes it hard when there's nothing I can do to help them . . . like this time with Colonel Sheppard. I'm always afraid of losing patients, but when it's a friend . . . But I can't live and work with them like we've done and keep them at arm's length. Maybe I should, but I can't."

Emira stood and walked around the desk to stand beside Carson, putting her hand on his shoulder. "I think I understand what you are saying. I'm glad we were able to use the medical pod to help the Colonel."

"Aye, me too," he said as he placed one hand on top of hers. "Thank you, Emira."

Emira grinned and tilted her head a little. "Perhaps you could . . . buy me dinner?"

Carson looked up her, confused.

"Something I heard Dr. Weir say to Colonel Sheppard one day when she had helped him with something."

Carson laughed and stood up to face Emira. "Well, I'd say that's the least I could do."

oOo

The next four weeks went by slowly, but the team was allowed to see Sheppard for a few minutes each day. They would take turns telling him about what they had been doing or telling about goofs made by the others. Once he figured out his presence was not seen as an intrusion, Radek began joining them once or twice a week. Carson was thrilled to be able to tell them John was showing signs of improvement after the second week in the pod. With the maintained reduction in swelling, the rods were removed from his head, much to Rodney's relief.

Five weeks and two days into John's stay in the medical pod, Carson found Emira already working in the containment room when he arrived at the infirmary. When he entered the room, Emira looked up from the control panel and smiled.

"Good news, Carson. I think the Colonel has healed enough to come out of medical stasis. His vital signs have improved and stabilized, the intracranial pressure is normal, and I think he's ready to breathe on his own."

"That is good news. What do we do next?"

"Well, I'm just double checking all the readings. If everything looks good, we'll get a medical team in here when we take him out. The change is sometimes a shock to the body, so we may have to help him a bit. Once he's stabilized into real time, we'll transfer him to a stretcher and integrate him back in the main infirmary. His body will only have done a few days worth of healing, so he'll still need a lot of care and he'll still be quite sore, but he should be out of danger."

"What can I do?"

Emira looked up briefly from her examination of the monitor readings. "Well, you could inform Dr. Weir and Captain Helia, and his team if you like. I can't have all them in here when we take him out, but they can wait outside if they want. We might have enough room for the Captain and Dr. Weir."

Carson nodded. "I'll just let them know."

An hour later, Elizabeth and Helia stood at the side of the room, watching as a medical team prepared to take John out of medical stasis. They had a gurney ready, as well as oxygen, a defibrillator, and other equipment, making Elizabeth more than a little nervous. Emira finally looked up at the team standing by and asked if they were ready. With a firm affirmation from the group, she pressed a key on the control console and looked over at the pod. Nothing happened.

Elizabeth glanced at Helia to see her response and noted the frown on her face. She then looked back at Emira in time to see her press more firmly on the key. Still, nothing happened.

Emira walked over and looked all around the pod and then shrugged her shoulders. "I have no idea why it will not eject. Let's try the manual override." She walked over to the side of the panel and opened a small door. Reaching in, she grabbed a handle and pulled it down. Nothing. Emira shook her head. "I've never seen anything like this. Call Dr. McKay in here and someone get Dolon."

A nurse left and returned a few minutes later with Rodney, who had been standing outside waiting with the rest of John's team. He was clutching his computer. "What's going on?"

Emira turned to him as he walked up to the pod. "The pod will not eject from the system and we cannot get Colonel Sheppard out until it does. Do you think you could find out what is the problem?"

Rodney smiled smugly. "Hello. Of course I can, genius here after all." He looked over the control panel and then sat down at the main controls. After studying it a moment, he hooked his computer up and began typing furiously. Several minutes later, Dolon arrived and went to see what the scientist was doing. Rodney briefly explained what had happened and what he was trying to do. Dolon nodded and sat down in the floor, removing a door to get to the crystals inside.

Rodney worked a few more minutes before looking over at Dolon. "Okay, I think we can reset the manual eject and then I can adjust the crystals, then we can try the manual system again."

Dolon nodded. "That might work. I'll reset the manual control." He stood and walked over to the door Emira had used earlier, opening it and pushing the handle back up into its original position. "It's ready."

Rodney moved to the floor and pulled out a crystal with each hand. He put the first crystal back in the second crystal's place, but when he went to add the second crystal, lap, waving his hand around and yelling, "Ow, ow, ow!"

The lights in the room suddenly went out, leaving it dark except for a faint blue light glowing from the pod and illuminating the pale patient inside. The eerie color made John look ghost-like. Emira and Carson had run to the pod when the lights went out, but both relaxed now that they knew the pod was still working.

"Thank goodness," said Emira.

Rodney was sucking on the end of two of his fingers when his eyes widened and his jaw dropped open. "That's not possible. That pod can't be working."

Carson snorted loudly. "Well, fortunately you're wrong. The Colonel is still intubated and if the power shut down without us able to get him out, he'd likely suffocate."

Rodney got to his feet and walked slowly over to stare down at Sheppard. "No . . . you don't understand. The power to this room can't be off and this pod still be working. It's sort of like at home when a breaker gets thrown. Everything on that breaker loses power. Everything in this room is powered by the same source. This isn't possible . . . unless . . . "

"Unless what, Rodney?" asked Elizabeth.

Rodney looked up at Elizabeth. "Unless it's being done on purpose. My God, he really is the favorite."

Carson sighed. "Rodney, you aren't making any sense. What's going on?"

Rodney had a peculiar expression on his face, like when he'd figured something out and still couldn't believe it. "I think I know why the pod won't eject and it's not a random malfunction. Atlantis won't let him go. She's shut off the power to the room as a way of telling us to get out while she holds Sheppard close."

Helia frowned. "Why would the city do that?"

Rodney shrugged his shoulders. "Not sure. Maybe it wants to make sure Sheppard doesn't almost get himself killed again. He's kind of habitual about that, you know. Or maybe she's just enjoying having him so close to her and she wants to keep it that way. Maybe it's a little of pile one and a bit of pile two, I don't know. All I know is that she's got him where she wants him and she's not letting go."

"There's got to be a way to get through to her. We can't leave John in there like that," said Elizabeth.

They stood thinking a few minutes before Rodney finally looked up. "Well, I might have an idea."

"What?" asked Carson.

"Maybe I could talk to her, convince her that Sheppard can't live like this."

Carson exchanged a look with Emira before looking back at Rodney. "And just how are you going to do that, with your Ouija board?"

Rodney rolled his eyes. "Don't be ridiculous, Carson. I thought you could do something with your sheep entrails." Rodney paused only a heartbeat before adding, "I'm kidding."

"Rodney," said Elizabeth forcefully.

"Right, sorry, I just thought the answer was obvious. Where does Sheppard seem to have all his heart-to-hearts with the city? From the chair, of course."

TBC

_Sorry to be short again. I leave for Albuquerque for the International Science Fair early in the morning and I wanted to get a little something posted so you would know I hadn't abandoned the story. Just been SUPER busy this week. I'll be gone a week, but then I'll get on this and finish it. Big apologies for the delay._


	18. Chapter 18

**Note: **For anyone still around, here is another chapter. The good news is I think I can post every couple of days until I finish. The bad news is that I did this one in a hurry and it's probably full of mistakes. By the way, Albuquerque is awesome!

The Return Part 2: Favorite Son - Chapter 18

Rodney stood looking down at the weapon's chair. He thought it ironic that after all his time spent envying Sheppard's ability to connect to Atlantis, now that it was his turn, he was nervous. Rubbing his hands together and giving a resolute nod, he turned and sat down. He concentrated on finding Atlantis, seeking out the city with his mind. The connection seemed rough at first, but finally slid into place as allowed his guard to slowly lower.

The sudden rush was almost dizzying as Rodney seemed to fly through the internal workings of Atlantis. He saw the city from totally new perspective, leading to a deeper of understanding of how she worked. He didn't even realize he was smiling as the thrill of the connection made him shiver. He'd connected to Atlantis through the chair before, but never like this. He had no idea what had made the difference, but he was grateful for it. Rodney thought he was just beginning to understand Sheppard's love and devotion for her.

He had no idea how long he wandered and drifted, touring his home from a different vantage point, but he finally remembered why he was here. He wasn't sure how to contact Atlantis, so he just began broadcasting, calling to her. And eventually, she answered.

It wasn't with words. He didn't actually hear a voice and the words were never directly spoken, by him or by her. The thoughts and emotions were just there.

_Why do you seek me? _

"I'm Dr. Rodney McKay. But I guess you know that. Well, of course you know that, you can see us and hear us, can't you. Okay, rambling here. Look, Sheppard is . . . our friend. And we're really worried about him. The doctors say he's ready to come out of the medical pod, but you won't let him out."

_He is hurt and I am caring for him. I can keep him safe so that he will not leave me as the others did._

"What others? Who left you?"

_There have been others who were my sons, my daughters, but they have been few. I can communicate with others like yourself, but my true children do not come very often. And then they leave and I am alone for a long time again. I need John. Together we can repair the city and make it great again._

Rodney could feel the sadness in the city's embrace. He almost felt sorry for her. "Look, I know you just want to keep him safe, but you can't keep him in that pod forever. What about when he gets better and wakes up? He's going to want out."

_John does not have to wake up. I can keep him asleep so that he stays with me. Together we can make sure the city and everyone in it is safe. I can provide for all of his needs._

"Do you want John to be happy? _Can _you want John to be happy? Because he won't be like this. Part of what makes him who he is is his energy. He has to be out in the action, protecting people and protecting you, risking his hide and playing Kirk to the women. If you keep him locked up in here, he'll quit being the John Sheppard we all care about. And he can do things from out here he can't do from in there."

The pause was so long that Rodney thought she'd left, or at least quit communicating with him. _He is getting restless, pulling away. _

"Told you. Uh, I mean, that's what I'm talking about. Sheppard's like a kid, he can't sit still. He has to be in the middle of things. You can't just pin him up and expect him to be happy. It won't happen. Let him go or he'll end up hating you."

_If I let him go . . . he will go away and not come back. The others wanted to help protect me and the people of the city, and they always went away. Can you make John safe?_

Rodney sighed, at least mentally. "Look, I can't guarantee Sheppard won't get himself killed. He kind of attracts trouble and disaster, as you've undoubtedly noticed. I can promise you that we will watch over him as best we can."

_You care for him. So do some of the others, the ones that were here before._

"Well, we work together and you kind of get used to him and . . . alright, yes, we care for him. Some of us have gotten close, like a family. Look, we worry about him too because . . . sometimes we're afraid he'll leave us as well. I've threatened to wrap him in bubble wrap and lock him in a closet more than once. But we care about him enough to let him be who he is, even if that means making us worry. Is any of this making sense?"

_It is odd, but I think I begin to understand. Logically, it would be better to keep him safe with me so he could be of the most help with the city. But then he would cease to be John Sheppard and might not be of any help at all. Either way, I will be alone again._

"No, you won't be alone. Sheppard loves connecting with you and working to fix the city. Heck, he just likes visiting I think. I can guarantee that he'll be here as often as you want him. And, I know I'm not one of your special ones, but . . . I'd kind of like to come back too."

_You are different. Our connection is different . . . and harder to maintain._

"I know, stupid fake gene."

_I do not understand._

"Oh, nothing. We call the part of us that allows us to connect with you a gene. I wasn't born with it, so our doctor gave it me artificially. It doesn't seem to work as good as Sheppard's. He's actually got three of these genes, which is why he's the favorite." Rodney could have sworn he felt her chuckle.

_You are interesting Rodney McKay. I think I would like for you to communicate with me again. I sense you care for the city and you know much about me. You are very wise and I will heed your words. _

Rodney felt his heart flutter for a moment. "You'll release Sheppard?" He had hoped his little talk with Atlantis would work, but he hadn't been sure he could get her to listen. His experiences trying to talk some sense into obsessed AI's were limited, at best. At least he guessed she was an AI. It worried him to think about what else she could be.

_I will release him. I charge you with seeing to his safety._

"Oh, thanks. Why don't you just give me the impossible job? I'll do what I can, but I'm not making any promises. Once Sheppard gets his mind set on something, it's hard to sway him away. But . . . I can promise that we'll do our best."

_Then I release him to your care._

"Thanks." But she was already gone. He opened his eyes as the chair moved back into an upright position to find Carson and Elizabeth watching him. He jumped. "Jeez, what are you people doing, trying to give me a heart attack?" he asked, dramatically placing his hand over his chest.

Carson sighed and rolled his eyes. "We wanted to make sure you were all right."

"The chair is fixed and I'm fine, thank you," he said as he stood up. The room wavered and darkened for a moment, causing him to sway slightly. "Wow." He felt a hand on each arm, steadying him. When is vision cleared, Carson stood on one side and Elizabeth on the other, both looking concerned.

"Rodney, why don't you sit back down a minute?" asked the doctor.

Rodney grinned. "No, I'm fine. Just a bit of a head rush from standing too fast. I did it. Ha! Sheppard isn't the only one Atlantis listens to any more. I convinced her to release him."

Elizabeth's eyebrows shot up. "You did? Are you sure?"

Rodney frowned, looking insulted. "What do you mean am I sure? Of course I'm sure. Carson, call Emira."

Carson shrugged his shoulders and tapped his radio. "Emira, this is Carson. Rodney says he convinced Atlantis to release the Colonel's pod. Can you confirm this?"

It was several seconds before Emira replied. _"He did it. The controls are working again. We're going to move the Colonel to the special care unit."_

Carson smiled. "Thank you. We'll be right there." He looked over to Rodney. "You're right, she let the pod go. I didn't know you had it in you."

Rodney just smiled smugly. "There's a lot you don't know about me. Let's go check on flyboy."

oOo

By the time they arrived at the infirmary, Sheppard had been disconnected from the pod and settled into a bed. Monitors displayed various readings about his condition and Emira stood studying them as they approached. Rodney was pleased by the fact that Sheppard had on an oxygen mask instead of being connected to a ventilator, although he was still terribly pale. The bandage around his head seemed smaller, although fading bruising was still evident on his face, arms, and the exposed part of his chest. He looked as Rodney would have expected him to look a few days after the explosion, not over five weeks later. But still, the man was alive.

"Emira, how did it go?" asked Carson.

The doctor turned to face them and nodded briefly. "Everything went smoothly this time. I think we have him settled in and he seems to be doing well at the moment. The pod will have been keeping him slightly sedated, so I expect he may regain consciousness soon. We'll have to be careful about pain maintenance the first few days. The change in going from the pod environment back into real time can be a shock to the body. The increase in metabolism and lack of sedation often triggers a startling rise in the pain level and we don't want it to get ahead of what the Colonel can handle."

"Well, you'd better be paying close attention because you know he won't say anything unless it's unbearable," commented Rodney.

Emira looked quizzically at Carson, who nodded. "The Colonel doesn't like pain medication and he has a rather high pain threshold. He usually won't tell you when he needs relief unless it's pretty bad."

Emira nodded in understanding. "Savill can be like that. It must be something about the military."

"Can I sit with him, you know, in case he wakes up?" asked Rodney.

Emira opened her mouth to respond and then stopped when she remembered her conversation with Carson. She thought for a second, and then gave a small nod. "I suppose that would be all right. You must agree to move if we need to get to the Colonel. His condition is still very serious."

"I can do that. I've done this enough to know the drill. I just don't want him to wake up and not know anyone. It can be kinda scary. Besides, I have to brag about convincing Atlantis to let him out."

"I'll let Ronon and Teyla know what's happened. Don't be surprised if they stop in later," said Elizabeth.

"That will be fine," said Carson. "I'll make sure they get to see the Colonel."

Elizabeth nodded and walked over to stand by John. Reaching out, she brushed her hand lightly across his bruised cheek. "Get better, John. We need you." She stood looking at him for several moments before turning back to the others. "Take care of him."

Not sure who she was talking to, they all nodded as she left. Emira touched Carson on the arm. "I must go report to Helia. She'll be relieved to learn the Colonel is out of the pod and doing well."

Carson nodded. "Thank you, Emira. Maybe we could have tea later and discuss his recovery, what needs to be done next."

"I would like that," replied Emira with a broad smile. Carson flushed slightly as they watched her almost bounce to her office.

"You two have it bad," mumbled Rodney, shaking his head.

"I have no idea what you're yammering about, Rodney."

"Oh please," Rodney said with a smirk. "You're both practically drooling. So, have you two gone around the pole with each other yet?"

"What?"

"You know . . . done the dance . . . committed the act . . . "

Carson let out a harsh groan as his face turned red. "That is hardly any of your business! And not at all an appropriate question to be asking a gentleman. You are the barbarian around here, so I'll not be hearing you call Ronon names any more, you . . . you . . . heathen!" Carson stormed off mumbling to himself under his breath.

"Didn't get very far yet, huh? Too bad." Rodney shrugged his shoulders and pulled up a chair beside John's bed. "I may have to give the Kirk designation to Carson if he keeps this up. You're slipping."

oOo

After a while, the warm comfort that has wrapped John begins to feel oppressive and he unconsciously begins to struggle against it. It fades away and he is suddenly cold and feels naked, exposed. Touches and noises fade in and out for a while, along with pain that is a changing, sometimes frightening creature. Over time, the sounds begin to sound more familiar, clearer. As they seem to get closer, the touches also begin to feel comforting and protective. His mind is not clear enough to understand what is happening, but he is relaxed in it. It feels right. It feels safe.

John gradually became aware that he was staring at the ceiling of the infirmary. He blinked and began to realize he could feel things. He could feel the invasive tubes, monitor electrodes stuck to his skin, bandages pressing down his injuries. Sudden silence made him aware that a clicking noise had stopped and he slowly turned his head a few inches on the pillow. Rodney sat with his fingers poised of the keyboard of his laptop, staring at him as if he were a ghost.

"Sheppard . . . are you really awake this time?"

John tried to answer, but his throat felt rough and sore and like it was clogged with something. He didn't get any sound out, but he did manage to spawn the coughing fit from hell. It made his head pound and his belly burn until spots danced before his eyes and everything faded away. When he was next aware of his surroundings, he felt cool liquid in his mouth, easing down his throat. Some blessed soul had slipped him an ice chip. He would have groaned with relief if he hadn't been afraid of trying to make any kind of sound.

"Colonel?"

When John opened his eyes, Rodney had moved to the background and Carson and Emira stood on either side of his bed, looking down on him with what he thought of as doctorly concern. Carson smiled when he John made eye contact with him.

"Don't try to talk just yet. I'm afraid you were seriously injured and you've been on a ventilator for a while. You should give your throat time to recover, so you may not be able to talk for a day or two."

John nodded. At least now he understood why his throat felt like it had been through a meat grinder.

Carson's smile broadened at John's response. John glanced around at the monitors and IV bag and back to Carson, frowning. With this much support equipment, the painfully obvious signs of head, shoulder, and rib injuries, and the knowledge that he'd been on a ventilator, John began to wonder what had happened. He concentrated, trying to dredge up some flash of a memory that would fill in some of the gaps. He had a faint thought of rocks and that was it. He needed to know what had happened and if anyone else was injured. Rodney was there, but what about Ronon and Teyla. He opened his mouth to ask.

"Ah, ah, ah!" scolded Carson. "Don't talk. I know you have questions, Colonel, but you need to rest your throat. Mouth the words silently and maybe we can make out what you are saying."

"What happened?" John silently asked, slowly and carefully forming his mouth around the words.

Carson moved over a little to make room for Rodney as he stepped up to the bed. The scientist briefly explained their mission and the events that had transpired on the planet. When he was finished, Carson turned back to John.

"I imagine you're curious about your injuries. You sustained a serious head injury, a skull fracture actually. Several ribs were broken and we had to operate to stop the internal bleeding. You've also broken your collarbone and dislocated your shoulder," Carson said as he nodded toward John's arm, secured to his torso with a sling.

John licked dry lips, fear and dread filling him at the report on his injuries. He was becoming more aware of the aches and pains that seemed to permeate almost every square inch. Carson seemed to notice his discomfort and slipped him another ice chip before continuing.

"Colonel, I'm afraid your condition began to deteriorate within the first twenty-four hours. There was swelling in the brain that resulted in a slow, but steady rise in pressure that we were having trouble controlling it. Emira told me about a medial stasis pod the Ancients sometimes use in cases of severe injury."

John's eyes widened and he could hear the sound of the heart monitor increasing steadily. The thought of being in one of the stasis pods scared him and he began studying the people around the bed, looking for signs of aging.

Carson picked up on the pilot's fear almost immediately. "It's not like the stasis pod we found the old Elizabeth in. Although it does slow down the metabolism, it's not nearly as much as the true stasis pods. It also provides precise monitoring and life support functions. It was able to provide for all your needs and make needed adjustments in medication and fluid levels as soon as they were required. I believe the medical pod is the reason you survived."

John forced himself to relax, reminding himself that these people would never do anything to hurt him. "How long?" he mouthed.

"You were in the pod a bit over five weeks, but to your body it was like a few days. You've been out for a couple of days now, but we've kept you pretty heavily medicated to help control the pain levels. The good news is that you are healing nicely. There is no sign of any recurrence of the internal bleeding or swelling in the brain. It may take a little while, but we believe you'll make a full recovery." Carson patted John gently on the arm that wasn't injured. "Don't worry about it Colonel. That pod is the reason you are alive and that's the most important thing."

John gave a small nod. "Is everyone else okay?" he asked, wheezing out a bit of air as he mouthed the words.

"Aye, everyone else is fine. Rodney had a cut, but it's all healed. Savill had a nasty bump on his head, but he's recovered as well."

John let out a long breath and relaxed even more. "You'd better get some rest, Colonel, because when I tell Ronon and Teyla you've finally woken, there'll be no holding them back. They just left not long ago after hanging around most of the last two days."

"Wait," said Rodney. "I still have to tell him about how I talked Atlantis into releasing him." Rodney grinned and pointed to his chest. "That's right, Sheppard, me. _I_ had a conversation with your precious city and guess what? She likes me. Even invited me back. You may have a little competition for that chair you like to spend so much time in."

John tilted his head a bit on the pillow and frowned in confusion. "What?" he tried to croak, producing very little sound.

"Rodney, you'd better not agitate my patient into trying to talk and ruining his throat," warned Carson.

Rodney stepped back and looked indignant. "What? This is _not_ my fault. Sheppard is the one not following doctor's orders, yell at him. He's just jealous."

John felt the comforting tingle of Atlantis and smiled. She had seemed distant for a while and he wasn't sure if she really had been, or if his perception had been off. But he felt her now and relaxed back into her warmth as he half listened to Rodney's somewhat lengthy monologue and watched Beckett inject something into his IV. The pain began to recede, becoming less sharp and more muted. His mind began to fuzz over, but it was a pleasant, comfortable feeling. He was surrounded by people and a city who cared for him, so gave himself over to it.

"Rodney."

"Wait just a minute Carson, I'm serious about this. Sheppard thinks he's the only one special enough to talk to Atlantis and he's not."

"Rodney."

"Now, granted, he makes the connection more easily and he does that thing where he looks all dreamy and he hasn't even been near the chair. I can't just touch the wall and feel her as strongly as he can, but you never know. You might figure out –"

"_Rodney!_" Carson whispered as loud as he could.

Rodney threw his hands up in frustration. "What? Crimony, Carson, you keep interrupting me."

"Colonel Sheppard is asleep."

Rodney looked down at the sleeping figure and almost smiled at how relaxed he looked. "Oh." He looked back up at Carson and noted how flushed the man's face had become. "Why didn't you just say something?"

TBC


	19. Chapter 19

The Return Part 2: Favorite Son - Chapter 19

John shifted a bit in bed, wincing at the stab of pain in his midsection.

"Better be careful there. Carson will have your hide if you rip out those stitches."

John was sitting propped up in bed with the tray table over his lap, a plate of soft food in front of him. It had been three days since he woke up enough to be coherent and remember the event. He was still encumbered by an IV and monitor wires, but at least he'd managed to rid himself of the oxygen support and catheter. Carson had agreed to remove the invasive tube when he informed John they would be getting him out of bed for a few minutes after his first meal of something thicker than broth. John reasoned if he could get out of bed for a walk, he could be helped to the restroom.

"They come out in the morning anyway, McKay." John swirled what looked like thin mashed potatoes with his spoon. "What is this stuff?"

Rodney pushed himself up slightly in the chair to peer over the edge of the tray. Making a face, he let himself slide back down. "You'll have to ask someone else. That was definitely _not_ what I had for lunch, thank goodness."

John rolled his lips in for a second, thinning them out in a grimace. "Gee, thanks for that. Are you sure you aren't needed in the lab?"

"Positive. Guess it's your lucky day."

"Yeah, right. Watery potato-like stuff and Rodney McSmirk. Lucky me."

Rodney smiled smugly as he studied the image on his computer screen. "I think I can boost Atlantis's shield and the distance we're getting on the drones."

John's attention strayed from the plate in front of him as he shifted his gaze suspiciously to Rodney. "Really?" he drawled. "How?"

"I've been running some ideas past Atlantis on reconfiguring one of the power grids and she thinks it'll work." Rodney purposefully didn't look up at John, choosing instead to keep his eyes on the computer.

"You've been talking to Atlantis?"

Rodney finally looked up. "Yes, I've been talking to Atlantis. You remember what I told you about communicating with her through the chair, right?"

John furrowed his brow and looked back down at the mush on his plate. "I remember. I just didn't realize . . . you were having regular conversations now."

Rodney chuckled and threw his head back. "You are so easy!"

"What's that supposed to mean?" John asked sharply.

"Don't worry, you're still the favorite. I practically wore us both out trying to maintain the connection long enough to explain what I wanted to do and then she told me it would have been more expedient to do it through the computer. Then, when she decided it would work, she informed me that you would have to initiate the changes from the chair because our connection isn't strong enough. So don't worry, I won't be stealing your place any time soon."

John tried to stifle the smile that threatened to spread across his face. He knew it was childish to feel this way and he really didn't want to get caught. "I wasn't worried."

"Whatever. You better eat before Carson comes back to check on you. Speaking of Carson, have you seen the way he looks at Emira?"

John took a small bite of the soft goo on his plate, making a foul face as he ate it. "Needs salt . . . or something." He shuddered and then grunted at the pain it caused. "And I think Emira is returning those looks right back at him. You think they're a couple yet?"

Rodney leaned forward a bit in his chair. "Oh, they're a couple, I'm just not sure what they're a couple of."

John slid his eyes sideways at Rodney. "Funny."

"No, no. I mean I'm not sure how far they've taken their new-found affections. I tried to ask, but Carson basically told me to mind my own business."

John turned to Rodney, his eyes wide. "You _asked _him? It's a wonder he didn't punch you out. You really need some people skills, McKay. Some things you just don't ask."

Rodney grunted. "That's what my third grade teacher said when I asked how old she was." He frowned when he saw John staring at him. "What? I was trying to figure out if she was old enough to remember World War II. I thought asking was the most efficient way."

"Hello, John. You are looking better," said Teyla as she, Ronon, and Savill approached John's bed.

Ronon nodded toward the plate. "Looks like you finally got some solid food."

John scooped up a spoon of white mush and turned it over, watching as the semi-solid slid off the spoon, dropping to the plate with a plop. "I'm not so sure about the solid part."

Ronon shrugged his shoulders. "Hey, at least they aren't feeding you through a tube."

John waggled his eyebrows. "That's true. However, feel free to smuggle me in something edible any time now. Preferably something that requires chewing before it's swallowed."

Ronon shook his head and sighed. "Not happening, Sheppard. Beckett's pretty tame most of the time, but he can be scary when you mess with his patients."

John let his gaze drift over to Savill. "Don't look at me. Emira's at least as bad. I learned early on not to get on her bad side. Sorry, Colonel, but you'll just have to survive on . . . whatever that is." Savill wrinkled his forehead and shook his head at the sight of John's plate.

"Well, thanks for the support. Whatever happened to not leaving our people behind?"

"That does not apply to the infirmary," said Rodney wryly.

They fell silent as Carson walked across the room and joined the little group. He watched John play in his food for a moment before sighing loudly. "Is he still complaining about his food?"

"Yes," the group chorused.

John picked up his spoon and once again let a gelatinous mass slide off the utensil with a splat. "Seriously, Carson, this is _not _food. I need something I can chew, preferably something with taste."

Carson crossed his arms and tilted his head slightly. "Colonel, you may feel hungry, but your system is not ready for anything more complicated or spicy than what is in your plate. You need to start processing bland, soft foods before we move you on or you'll just set yourself back. And you've done this enough times to know that. Now stop whining and eat your mush like a good little boy, or we'll get out the feeding tube and go that route."

John rolled his eyes and scooped up a spoonful of food. "Fine, fine, I'm eating. See?" He put the food in his mouth and then made a series of faces that ended in a smile that came out more of a grimace. "Mmm, tastey." He grabbed his glass of water and drained half of it.

Carson smiled smugly and gave a nod. "Much better, Colonel. Now finish your lunch so we can take you for a short stroll around the infirmary."

"Somehow my day just keeps getting better," murmured John.

"Anything has to be better than being crammed into the medical pod," shuddered Rodney. "Do you remember anything about being in there? Were you ever aware you were in the thing?"

John set the spoon down, looking a bit uncomfortable with everyone staring at him. He shrugged his shoulders slightly. "I don't really remember anything. I . . . kind of have some vague . . . impressions, feelings."

"Like what?" asked Carson, his expression curious.

John grimaced, trying to figure out how to put thoughts and emotions that seemed distant into words. "I don't know, just . . . sometimes I felt kind of alone . . . but then other times I felt warm and . . . comforted . . . kind of like I was wrapped in a really soft, blanket."

"Atlantis," said Rodney.

John rubbed the back of his head, frowning. "After a while, it seemed like the blanket was wrapped too tightly, like I was smothering. I felt . . . restless and trapped. I wanted out."

"That was probably about the time Rodney was talking Atlantis into letting you out of the pod," said Carson.

John nodded. "I guess, because shortly after that it seemed like I was free. But then I was cold, I felt kind of alone. The pain kicked up about then too, I think. Then it was just a blur of noises and touches, but eventually that feeling of being safe and taken care of returned. And this all sounds very weird and I have no idea why I'm telling you this."

Rodney grinned. "Because we asked."

John took a deep breath and let it out slowly. "Yeah, you did." He looked up at Carson. "I'd like to see this medical pod."

"I thought you would, but you need to wait until you're stronger. I'll show it to you and explain how it works."

"Thanks." John gave a small smile. "Guess I'd better eat my gruel so I can go for my walk."

Teyla moved closer to the bed and picked up John's hand, clasping it in her own. "It's good to have you back, John. We missed you."

John blushed slightly, pushing the rush of emotions down deep. "It's good to be back."

oOo

"Well, how'm I doin?"

Carson looked up from the chart and smiled. "Very well, Colonel. Your injuries are healing nicely, you're regaining your strength, no sign of infection. I'm a little concerned about the lingering headaches, but even they seem to be diminishing of late."

"So, I can get out of here soon, right?" John tried not to look overly eager, but he was pretty sure he was failing miserably.

Carson chuckled. "In a day or two. I'd like to keep an eye on you for a bit longer. Can't have you passing out in your quarters with no one the wiser. You have to understand that your head injury was very severe and you may experience some lingering effects for a while longer."

John sighed loudly. "I know, but I can be careful. It's not like I feel like running any marathons anyway. I'd just lie around my quarters, maybe read or something."

"Not just yet. I can take you for a small field trip, though." Without explaining, Carson turned and headed across the infirmary. John sat up straighter in bed, straining to see where the doctor went, his curiosity roused. Carson returned a couple of minutes later with a wheelchair, parking it beside the bed.

"All right, let's get you into the wheelchair and I'll take you for a little tour," remarked the doctor as he helped the pilot out of bed and into the waiting chair. Once John was settled, Carson took him through three sets of doors to a room so far back in the infirmary, John hadn't realized it was there.

"This is where the medical stasis pods are located," explained Carson as they entered. John could see several pods scattered around the room, each with a control panel. Carson pushed some panels on one and the pod slid out of the wall, the clear top opening to reveal the interior.

John looked inside the pod for a moment, studying it. "It looks kind of like the pods on the _Aurora_."

Carson nodded. "That's what Rodney said. When we hook you up to the pod, it gives full medical support. It monitors everything from heart, blood pressure, temperature, brain waves, and blood chemistry to intracranial pressure if you want it to. It supports IV systems, transfusions, adds appropriate medications, and has a ventilator connection if needed. The monitoring is so precise and efficient, that is provides much better critical care to patients than a nursing staff can. This is what kept you alive, Colonel."

John stared at the pod silently for several minutes before saying anything. "I was in there for five weeks?"

"Aye, five weeks and two days."

John grimaced and licked his lips. "I'm glad I was unconscious."

Carson nodded. "The pod is set up to slow your metabolism down quite a bit to give your body more time to adjust to the injuries and heal. That alone makes waking unlikely. But in the event an occupant begins to show signs of waking, the pod automatically keeps you sedated enough you won't. It would probably be scary to wake up trapped in one of these things."

"I think that may be an understatement."

Carson looked at John and smiled. "Your team missed you, Colonel."

John glanced up at Carson and creased his brow a little. "I think maybe I missed them too."

Carson clapped John on the shoulder and smiled broadly. He then began to point to various controls and explain how the pod system worked. Within a few seconds, he was enthralled with the technology all over again in his attempt to make John understand what the pod was capable of. After several minutes, John frowned deeply and cleared his throat.

"Doc, look, I don't mean to be rude or seem ungrateful or anything, but this is the point where I usually stop McKay and tell him this is so far over my head that I don't understand half of what he just said and, to be honest, I don't want to understand it any better than I already do. I'm afraid I don't want to understand this either. I trust you. If you thought I needed to be in that pod, than I'm not going to argue or second-guess you. Could we just leave it at that?" John looked hopefully at Carson, not wanting to hurt his feelings or make him angry.

Carson nodded as he laughed. "All right, son, I can understand that. I've had the misfortune to sit through a few of Rodney's detailed explanations of technology I couldn't pretend to understand, so I think I know how you feel. And I won't hold it against you."

"Thanks, doc. I hated to cut you off, but the details of how it monitored and took care of all my bodily functions was just a bit much."

"Well, then, if you don't have any questions . . . "

John glanced back at the pod and grimaced again. "No, no questions. I think I've seen all I want to see and heard all I want to hear."

Carson nodded and pushed the button that retracted the pod back into its chamber. Turning the wheelchair around, he headed back into the main part of the infirmary. "Let's just get you back to bed, then."

John groaned out load. "I just got out of bed. Look, the guys are supposed to be here in a minute to visit. Can't I just stay in the chair and they can take me out on the balcony for a few minutes to see the sun and smell the fresh air. I feel like I haven't seen the sun in weeks. Oh, actually I haven't seen the sun in weeks."

Carson considered it as he pushed the chair along. "I guess that would be all right, as long as you stay in the chair. A little fresh air might be good for you."

John held up his hand. "I'll stay in the chair, Scout's honor."

Carson rolled his eyes. "We'll not be going into that. Just give me your word that you'll stay in the chair and come back when I say."

"I promise, Carson. I just need . . . to get out of here for a few minutes."

They entered the infirmary to find the team already waiting and looking a little worried.

"Where were you?" asked Rodney sharply.

John pointed back to the doctor. "Carson took me on a tour of the medical pod room. Cozy."

As Carson stopped the wheelchair, Teyla nodded to John. "I'm glad to see you are getting around. Does this mean you feel better?"

John nodded his head, realizing that he really did feel better than he remembered feeling in a long time. He was still sore, but wasn't really in pain as long as he didn't move too much or too quickly. Even his headache had laid low for the day. "Actually, I do feel better, thank you. Carson says I can even go out on the balcony if I stay in the chair and we don't stay too long."

"I push," said Ronon, moving to take over Carson's position.

"Wait, wait, wait," said Carson. "There are a couple of conditions. First of all, the Colonel must stay in the wheelchair. Second, Ronon, no popping wheelies or having chair races with the Colonel. He's not finished healing yet and I don't really want to have to start all over with a new set of injuries."

Ronon looked disappointed, but gave a small nod. "Okay, no wheelies or anything else fun."

Carson looked unsure, but nodded anyway. "All right then, twenty minutes. Bring him back earlier if he starts getting tired." He picked up a blanket and spread it out over John's lap as the pilot frowned at him.

"Carson, I'm not cold."

"No, but as I recall, it's a bit windy today and I don't want you getting chilled while you're out there."

John sighed and looked up at Carson. "Thank you, _mother._"

"Get him out of here," said Carson. "Before I change my mind."

Ronon wheeled John toward the door to the infirmary, the rest of the team trailing behind. As they turned into the hall, John glanced back behind him and made eye contact with Carson. "Thanks, Carson," he said just before they disappeared from view.

Carson snorted softly. "You're welcome, Colonel, as always."

TBC


	20. Chapter 20

The Return Part 2: Favorite Son - Chapter 20

John heard Rodney before he actually saw him. Sitting on the edge of the infirmary bed, he listened to the scientist's voice drifting down the corridor.

"I'm coming, I'm coming. I know I'm late but it's really not my fault." Rodney rounded the corner, huffing and puffing as he hurried across the room. "Radek pulled me in with some inane question that led to whole debate, knowing I was supposed to meet you here. So, are you ready to go, we need to get out of here."

John grinned and shook his head, his mind trying to process the fast talk. "Calm down, McKay, where's the fire? Carson hasn't dismissed me yet anyway."

Rodney glanced nervously around the room and then looked at his watch. "Well, where is the sheep herder? We need to get you out of here. You were supposed to be released already."

"Rodney, calm down. You're walking me back to my quarters, which is totally unnecessary by the way, not escorting me to the ball. Why does it matter what time we get out of here? I get to lie around and read or watch DVDs for the next week. I'm not in a hurry."

Rodney looked flustered for a minute, making John wonder what was going on with him. He was about to ask just that when they spotted Carson rushing across the room. "Okay, Colonel, your last scan looks good, so you're free to go." He turned to Rodney and gave a curt nod. "Hello, Rodney."

"Well, it's about time, Carson. We're on a schedule here, you know."

John frowned at the knowing glances the two men were giving each other. "Guys . . . what's going on?"

Carson turned back to John. "You're free to go Colonel. Just take it easy, as we discussed earlier, and let me know if the headaches get any worse or any more frequent. Barring any new problems, I'll see you in a week."

Rodney nodded enthusiastically and grabbed John's good arm, his other still in a sling. "Okay, Sheppard, come on. We need to move."

John sighed, noticing the two men had ignored his question. "Rodney, I'm in scrubs. Let me change first."

"No, no, no, your clothes are in your room. It's not like you're in a gown or something. Scrubs are fine. Now come on."

John slid off the bed, pulling his arm away from Rodney's grasp. "I'm coming. But you're telling me what's going on here, one way or another." He barely kept up as he followed Rodney out of the infirmary and down the hall. He wanted to yell at the man and demand answers to his questions, but it took all his breath to hurry down the hall and not get left behind. By the time they reached his quarters, John was pretty sure he would have to sit down to keep from collapsing. He stopped in the doorway.

"Quit standing in the door and get in here. You need to get changed so we can go."

John took a few slow steps into the room, never taking his eyes off the bed. His dress uniform was laid out, looking as if it had been recently cleaned and pressed. John's face tightened into a scowl. "I want to know what's going on and I want to know _now_." He stared at Rodney, his expression firm as he tried to keep from panting in exhaustion.

Rodney rolled his eyes. "Fine, the Ancients want to do some kind of thingy to honor you."

John narrowed his gaze, his unease rising. "Why?" he drawled.

"You know, for leading the raid that retrieved Atlantis and then for saving all our lives on that planet, when the outpost blew up."

John frowned and shook his head, still not understanding. "Taking back Atlantis was a team effort between us and them. And I didn't do anything special on that planet. If anything, Teyla and Savill did all the work getting you guys out safely, not me."

Rodney laughed and shook his head. "Oh, no, no, no, my friend. You don't know, but you staying behind in the chair to try and stop the overload ended up buying us enough time to get out. Dolon and I went over the information we got on our computers before all hell broke loose and that whole place should have gone up in less than half the time it took. Whatever you did delayed the explosion long enough for the rest of us to make it out."

John dropped into the chair he was standing next to, his mouth open. "I didn't know. I just wanted to stop it if I could, save the outpost and hopefully all of along with it."

"Yeah, well, you saved all our lives and almost killed yourself in the process. I think Helia was impressed, and I get the distinct feeling it takes a lot to impress her. Anyway, we're going to be late if you don't get a move on." Rodney picked up John's pants and handed them to him. "Change."

John took them and slowly got to his feet. He looked at Rodney expectantly for a few moments before speaking. "Well, turn around."

Rodney rolled his eyes again and turned around. "You know, you're kind of shy for a military guy. I thought you guys lived in giant barracks and changed in front of twenty people all the time."

"I'm not shy. There's a difference between being shy and not being an exhibitionist. Just because I had to change clothes with an audience for a lot of years doesn't mean I enjoyed it. Besides, I haven't had to do that in a while. We have a little more privacy here in Atlantis."

"Unless you're in the infirmary, and then you have no privacy."

John bit his lower lip for a second. "True. But I'm not in the infirmary any more and I don't plan on going back any time soon."

Rodney chuckled. "Yeah, good luck with that."

"Thanks for the vote of confidence. Uh, Rodney, I could use some help." John had managed to change into his pants, but he couldn't seem to get the sling unhooked so he could change his shirt. Rodney sighed and began helping him remove the sling. Several minutes and a few groans later, John was dressed in his uniform. He put on his hat and faced Rodney nervously. "Well?"

Rodney put his right hand under his chin, propping his elbow on his crossed arm. "Not bad I guess," he said noncommittally. Dropping his arms, he waved at John. "Come on, we're still going to be late."

John followed Rodney out the door, wishing he was climbing into his bed instead. He hated being the center of attention, unless it was telling a good joke or something equally inane. He was embarrassed at the prospect of people honoring him because he didn't feel like he'd done anything special. If they wanted to do something special for someone, they should be honoring Elizabeth, Rodney, Savill, or Teyla, anyone but him. The knot that had been building in his stomach grew and tightened and he suddenly felt like he was going to hurl right there in the hallway.

John looked up to see Rodney almost to the next turn. He knew he needed to speed up to catch the physicist, but he was almost out of steam. The fast trip back to his quarters had taken a lot out of him and now he was running on fumes. He felt weak and he hated that more than almost anything. He stopped and leaned against the wall, his legs shaking a bit as he gasped for air. His head was beginning to pound and he still felt like he might puke. Maybe he could have Rodney tell them he wasn't up to this.

"Sheppard, are you all right?"

John looked up into Rodney's worried face. "Catching . . . my breath. Maybe . . . this isn't . . . such a good idea."

"Nonsense, just take a minute. I should have realized and slowed down. Sorry about that."

Okay, Rodney was being nice to him. Now he was really scared. "Rodney, I really . . . don't feel . . . so good. Maybe . . . you could just . . . tell them for me."

Rodney's eyes widened. "Oh, no, you aren't weaseling out of this, mister. This is a big deal and they've gone to a lot of trouble and you're going."

John winced and frowned, his stomach flipping in a very uncomfortable way. "Not helping."

Rodney slapped himself in the forehead with a gasp. "That's it. I can't believe I didn't figure it out earlier. You're afraid."

John scowled. "Am not," he barked.

Rodney smiled smugly and gave a short nod. "Yes, you are. Colonel Sacrifice-myself-for-everyone-else is afraid of a little awards ceremony."

John pushed himself away from the wall, anger pushing aside a little of the fear. "I have no idea what you're talking about, McKay. Are we going or not?" He took a deep breath and tried to calm his stomach and shaking limbs as he began walking unsteadily down the hall. He thought he heard Rodney snort behind him.

When they arrived in the control room a few minutes later, the fear came back with compounded interest. He stopped so suddenly that Rodney almost ran into this back. The control room was lined with Ancients dressed in what appeared to be their formal uniform.

"Move forward," came Rodney's whispered voice from behind him. "You can do this. It's a lot less painful than getting blown up, I promise."

John might have laughed if he hadn't been almost paralyzed with fear. He concentrated on putting one foot in front of the other, moving toward where Helia, Savill, and Elizabeth stood waiting for him. He almost faltered when he saw Jack O'Neill standing beside Elizabeth. What was he doing here? As he got closer to them, the view of the gateroom below opened up and he saw even more Ancients standing at attention. Now would be a good time for an earthquake or maybe a Wraith attack. He glanced back, looking for Rodney, just in time to see the man take up a position beside a bored Ronon and a smiling Teyla. Rodney gave him a big thumbs up, making John groan inwardly.

Turning back around, he took a deep calming breath. Rodney was right. He could do this. Elizabeth smiled proudly and even General O'Neill wore a happy smirk on his face. Savill gave him a slight nod as he stopped before Helia and stood at attention. Helia turned toward one of the techs and nodded, prompting the man to dial up the gate. John wanted to ask what was going on and what was he supposed to do, but his mouth was too dry to speak. As the wormhole was established, the screen came on to reveal General Landry on the other end. The woman at the controls informed the General they were ready to begin. John glanced around wondering where that Wraith attack was when you needed it.

"Lt. Colonel John Sheppard of the United States Air Force of the planet Earth." Helia's strong voice startled John and he flinched slightly, earning him a bemused look from Elizabeth and General O'Neill.

"You have proven yourself loyal and true, not only to your own people, but also to the city of Atlantis and our people as well. You have been willing to sacrifice yourself to save others and to preserve our home. Twice your actions have been above and beyond what can reasonably be expected, even to the point of serious injury to you. Your efforts have been witnessed by many and cannot be questioned. In order to show our appreciation, especially in light of the fact that you are not even of our people, we bestow upon you our greatest honor, the award of the star cluster."

John stood at full attention, almost unable to breathe, as Helia turned and took the silver cluster of five stars from the box held by Savill. She stepped forward and pinned them to John's uniform and then briskly stepped back. John glanced at Savill to see a small, approving smile on his face. That somehow made him feel better and a tiny bit of tension flowed away, allowing him to breathe. His gaze fell and he saw the same silver cluster of stars on Savill's formal uniform. Lifting his eyes to meet Savill's, the Ancient gave him an almost imperceptible nod.

"Lt. Colonel Sheppard." General O'Neill's voice drew John's attention back to the ceremony at hand and he looked at the officer, who had stepped forward a few inches. "The President wanted me to convey his congratulations on receiving this honor and tell you that you have represented our planet and our country well. He also wanted me to thank the Ancients for allowing us to work with them in the city. We got off to a little bit of a rough start, but he hopes this means we can continue to work together for a long time." O'Neill had turned to face Helia, but now turned back to John with a smile. "Basically, good job, kid."

"Thank you, sir." John saluted O'Neill, who returned the action and then stepped back into the line of people.

Helia turned to the screen behind them. "General Landry, did you have anything to say?"

Landry nodded. "Yes, as a matter of fact I do. Sheppard, I'm glad I was wrong about you. You're doing a good job out there, son. You can expect our full support with anything you need."

John nodded. "Thank you, sir," he managed to croak out before saluting. He hoped they were almost done, because between the stage fright and the increase in activity over what he'd been used to lately, his legs were beginning to tremble.

Helia turned back to face John and locked eyes with him. "When you first arrived, I was suspicious of you and your friends and your motives for helping us. I suspected you were out to take Atlantis for yourselves, but you have proven your honor and loyalty many times over. You and your team are granted the designation of true citizens of Atlantis, which means you have all the rights afforded any of my people. If relations between us and Earth falter, you will not be sent back unless you choose to go. And Colonel Sheppard, you are hereby granted honorary status as an officer in our forces. You are not compelled to serve in our forces, but you may choose to serve with us when the need arises. Savill can give you more information later."

John nodded, concentrating on breathing evenly and keeping on his feet. He didn't think collapsing into a puddle would look very manly or heroic. He wasn't sure if he was supposed to speak or not, but he felt stupid just standing there. "Thank you. We will do our best to live up to your expectations."

He guessed it was all right to talk because Helia just gave a small nod and seemed pleased with his response. "I know that you will. We are happy to share Atlantis with people who love and respect her as we do. Now, let us celebrate our newest citizens. This assembly is dismissed."

John raised his hand in a salute to the group before him and was surprised when Savill mimicked his moves, returning the salute with a grin. Voices erupted all around him as the formal air dissolved and casual conversation and laughter ensued. John's head was swimming and his legs were genuinely quaking now as he searched the area for a chair. A strong hand gripped his good arm and he looked up to see Carson hanging onto him.

"Lad, you look like you're going to pass out. You're white as a sheet."

John felt a bead of sweat run down the side of his face, ticking his skin. "Just a little shaky right now. See any chairs?" 

Savill arrived with a chair from one of the offices and set it down behind John. Carson helped him ease down into it and then kneeled beside him. "I told them they needed to give you a few days more, but they were anxious to do this. Tell me how you're feeling." 

John took a deep breath, relaxing into the chair, his entire body trembling. His vision had darkened, especially around the edges, and there was a loud buzzing in his ears, masking the words flowing around him. For a few seconds he thought he was going to pass out after all, and then his head slowly began to clear. He became aware of a hand on his uninjured shoulder, holding him upright. Blinking, he brought the room back into focus just about the time the buzzing faded away.

" . . . think he was ready for this. You should probably have them send a gurney."

"No." John lifted his drooping head and sat back against the chair. "I'm okay, I don't need a gurney."

Carson looked back at John, frowning slightly. Elizabeth and Helia stood behind him looking worried, along with O'Neill. Rodney, Teyla, and Savill stood on his other side, also watching him closely. Looking down at the hand on his shoulder, he realized Ronon was behind him. He looked up at the warrior. "Thanks, big guy, but I'm okay now."

John was relieved when Ronon nodded and let go of him. He turned back to the crowd around him. "I'm fine, now, really. I think I just did too much too fast. Just give me a minute to catch up and I'll be fine." And he was feeling better. Between the main event being over with and getting to sit down, he could feel the nervous tension from before leaving and his stomach settling. Someone handed Carson a glass and he passed it on to John, who drank greedily. The water sloshed a bit from the slight tremble still in his hand.

"Not too fast, Colonel," warned Carson.

John paused and then forced himself to drink more slowly. By the time he handed the glass back to Carson, it was almost empty. "Thanks."

"I'm sorry, Colonel," said Helia. "I guess we should have listened to Dr. Beckett and postponed this for a while. We've had it planned for a while and we were waiting on you to get dismissed from the infirmary. Dr. McKay suggested we make it a surprise."

John looked over at Rodney, who shrugged and waved. "Oh, he did, did he? I'll have to think of an appropriate way to repay him." His voice was level, but he was pretty sure from Rodney's expression that he got the true meaning of his words.

"That's not really necessary," squeaked Rodney.

"Yes . . . it is." Ronon laughed and Teyla gave John a look that was probably supposed to warn him to be good, but he ignored it.

"There is a reception prepared if you feel like attending. It is to celebrate both your award and the new status of your team," said Helia.

John nodded. "Thank you. We really appreciate everything you've done."

Helia smiled and shook her head. "No, Colonel, it is we that appreciate you. That's the purpose of today's activities. I must go to the reception now and I hope to see you there. But if not, congratulations Colonel Sheppard."

"Colonel, if you feel like you can walk, we should at least get you back to your quarters," said Carson.

John frowned and shook his head once. "No, I'm going to the reception. I'm fine, now that I've caught my breath. Hey, you think they have punch and cookies?"

Carson looked unsure. "I don't know. You came very close to passing out on us, Colonel. I think maybe you've had enough excitement."

John sighed and smiled, the knot in his stomach almost gone now. "That's just it, Doc. I've made it through the exiting part. Now I just want to relax in a chair and visit and eat some goodies. Then I can go back to my quarters and nap all I want. Come on, I can't skip my own reception. Don't want to offend anyone."

"He has a point," said O'Neill. "Let the man eat some cookies. We can keep an eye on him."

Carson stood and looked down at John. "I guess if you're sure you feel like it. I want someone with him at all times and making sure he makes it back to his quarters."

"We will stay with John and make sure that he is all right," promised Teyla. "Will you be at the reception?"

Carson nodded. "Aye, I think Emira is going to sneak out for a bit and join me there."

John tried to smother the grin he felt coming. "There, see. If anything goes wrong, you'll already be there." Then he added quickly, "But nothing will . . . go wrong, that is."

"All right, Colonel. You can go to the party. Then I want you to rest."

John grinned as he began standing, Carson helping him out of the chair. "Don't worry, Doc. Resting is probably all I'll have the energy to do." He looked over at O'Neill. "General, I have to admit, I was surprised to see you here."

O'Neill nodded. "Me too. Helia contacted us a while ago about this and offered to let us send someone as a representative if we wanted. The President thought it was a good idea for the Air Force to be represented for something that sounded like it was really important to the Ancients. It seems he was right." Jack grinned. "Plus, maybe I'll get some really good cookies out of the deal."

The whole group began walking slowly down the hall, following the other people who were walking in small groups toward the reception. "That's what I'm hoping, sir," said John.

An hour later, John sat at a table with Ronon, Teyla, and Savill. Elizabeth and General O'Neill were mingling and John was grateful that he wasn't expected to since he'd been told to stay put. Emira and Carson were two tables over, their eyes hardly leaving one another as they talked. Rodney ended up sitting with Radek and Dolon and the three of them hunched over a computer screen while eating what appeared to be some kind of cookie bar. The taste was different than anything he'd encountered, but John liked them and so did everyone else.

"Don't they ever relax and have fun?" asked Ronon.

"Who?" asked John, scanning the room for someone who didn't seem to be having fun.

"McKay and those other guys."

John chuckled as he looked at the three. "They _are_ having fun, big guy. They're geeks, this is how they relax."

They watched a few seconds and Rodney yelled, "Yes," and gave Dolon a high five, followed by Radek. Then they all began to point and talk at the same time.

"I see what you mean," said Ronon.

"I've never seen Dolon this animated about anything," commented Savill. "I honestly don't think there was anyone that could keep up with him until now."

"Yeah, same for Rodney, except maybe Radek. I guess they're the three scientific musketeers." John noticed that no one else at the table got the reference. "Never mind." Sometimes working with a bunch of aliens just wasn't any fun.

Ronon stared at the silver star cluster on Savill's jacket. "So, how big a deal is this silver cluster thing?" he asked, nodding down at the metal.

Savill sobered immediately. "It is a very great honor. Colonel Sheppard is only the fourth person I have seen or known to get the cluster. It is not given lightly and cannot be earned with a single action. One must truly prove his worth before he is even considered. Only a few are awarded each generation."

Teyla smiled. "Then we are very honored to sit at a table with two such warriors."

Savill grunted. "Well, while I'm honored to have mine, I have never felt worthy. I still do not understand why it was given to me."

John nodded. "I know what you mean. I kept waiting on someone to object, to say I was . . . " John shook his head. "I didn't do any more than anyone else did. If they wanted to award someone for being brave or smart or honorable, they should have given the thing to Teyla."

Teyla smiled and placed her hand on John's forearm. "I do not agree. They gave it to the right person. Why do you find it so hard to believe that you are deserving of this?"

John just looked at the table, the voice of his father and of several of his commanders echoed in his head, telling him how worthless he was. He closed his eyes and leaned his forehead against his hand. "I'm tired," he whispered.

A strong hand gripped his shoulder, causing him to look up. Ronon and Savill were standing on either side of him. "We'll walk you back to your quarters," said Ronon, moving his hand from John's shoulder to his arm to help him stand. John let him. He didn't feel like fighting it and he wasn't entirely sure he could do it on his own. Once on his feet, however, he did pull away to walk on his own. He caught Elizabeth's eye as they left and gave her a short nod. Her smile almost embarrassed him. She was so proud of him and he felt like such a fraud.

They walked slowly and quietly all the way to John's quarters. He was comfortable with them. They didn't rush him or worry over him. They seemed to know that he didn't want to talk. Stopping when they reached his quarters, he turned to face them. "Thanks for the escort. I think I'll just go lie down for a while."

Savill caught his arm as he started to turn away and stopped him. "I don't know what people in your past have told you, but if anyone deserves the star cluster, it's you. I haven't known you long, but I've seen enough to be certain of this. Don't you let anyone, past or present, convince you otherwise."

John took a deep breath, trying to silence the old voices in his head. He tried to make himself believe what Savill was saying. It wasn't that he really believed the naysayers from his past. He knew he wasn't worthless and that generally he did a good job. He'd saved a lot of lives over the years. But he'd also been responsible for some losses as well. A sea of faces haunted his nightmares, accusing him of failing them. The faces sometimes ganged up with the voices to make him wonder what he was doing.

"John?"

His head snapped up to look at Savill, and he gave a small smile at the man finally using his first name. "I'm working on it."

Savill nodded. "Get some rest."

Teyla stepped closer and leaned her head forward. He bowed his head to meet hers, resting there for a second before straightening up. "Thanks, guys. I'll see you later."

Opening his door, he walked in and let it slide closed behind him. He struggled for a while to get out of his uniform and into sweats and a t-shirt. By the time he laid down, he was completely exhausted. He wasn't sure whether to be excited by the events of the day or depressed by the voices telling him he didn't deserve it, so he tried to ignore all of it and get some rest. It wasn't long before a familiar feeling of comfort began to wrap around him, pulling him into its embrace. He smiled as he felt himself begin to relax and feel worthy, at least for the moment. "Thank you, Atlantis," he mumbled as he drifted off to sleep.

TBC


	21. Chapter 21

**NOTE:** Special thanks to Ginnia for the suggestion that the team show Helia their trust through a plaque. I thought that was a great idea, so I incorporated it into this chapter. And you'll be thrilled to learn that this is the last chapter. Thanks to anyone still reading.

The Return Part 2: Favorite Son - Chapter 21

John paused as he walked by his dresser, staring down at the black box. Taking a step closer, he reached down to open the lid. Light glinted off the silver cluster of five stars, one in the middle surrounded by the other four. He let his finger glide gently over the smooth surface, its meaning filling him with a sense of pride. He'd spent a lot of the last two weeks thinking about his life and what he'd done with it. Although he still had his disappointments and failures that he'd love to be able to go back and change, he'd decided that just maybe he was more of an asset than a liability. Elizabeth and Helia had both offered him nothing but support and he respected the leadership ability of both. He may not always make the right decision, but he was always willing to do whatever it took to protect the people around him. Smiling, he closed the box and took a deep breath.

A knock at the door drew his attention and he thought it open. Rodney strode in, finishing a conversation on his radio as he waved. " . . . us know when they dial in. Hopefully we'll be done by then. Right, that will work." Rodney clicked his radio off and glanced at John. "Okay, you ready?"

John nodded. "Yeah, I'm ready and looking forward to doing something constructive. I'm sick of reading and resting and going to PT." He unconsciously flexed the fingers of his left hand and then rubbed his shoulder.

Rodney cocked his head slightly and narrowed his eyes. "You _did_ clear this with Carson, right?"

John rolled his eyes and sighed. "Yes, I'm not a total moron. He said we needed to limit the time in the chair to two hours. If we aren't done, I can take a two hour break and then do two more hours. Until I'm released to full duty, that's all he'll allow."

Rodney nodded. "That should be fine. Two hours should be plenty. Besides, the new people are arriving about noon, so we'll need to quit then anyway."

"Good. The package should be coming with them. I hope our little idea pans out okay."

Rodney shrugged his shoulders. "Either she appreciates it or she doesn't."

"Yeah, I guess. Let's go." John followed Rodney as he led the way out of his quarters. They talked as they walked, arriving at the chair room a few minutes later. Dolon and Radek were waiting on them.

The Czech scientist pushed his glasses up as he lifted his head and watched them come into the room. "Look who decided to join us. We thought about sending search party."

Rodney just gave an irritated smirk as he went to the control panel and began checking readings. "Ha, ha, Radek, very funny. Don't quit your day job just yet. Oops, that's right, this is your day job. My bad."

Radek muttered something in Czeck, prompting a smile from John and Dolon. John coughed to cover a small chuckle and then looked at Rodney. "Hey, you want me in the chair yet?"

Rodney waved a hand dismissively at him. "Yes, yes, go ahead and connect. I'll let you know when to start doing stuff."

Dolon rolled his eyes for John's benefit and the pilot grinned as he sat in the chair, activating it as it slid back. The connection faltered for a few seconds, almost sputtering and making John reach out to seek Atlantis. He was instantly worried that something was wrong. He finally felt her and concentrated hard on making a thorough connection. Almost immediately, he felt an overwhelming sense of sadness. If he'd thought it possible, he would have thought the city was crying. He reached deeper, seeking the reason for the flood of emotions, only to encounter guilt and fear. Calling out to Atlantis, he questioned what was wrong.

A short time later, he finally understood. Atlantis was apologizing for holding him in the medical stasis pod and seemed almost fearful of his response. He sought to comfort her, in much the same way she had comforted him in the past. Doing his best to assure her that he wasn't angry, he pushed acceptance and understanding toward her. He wanted her to know he understood what she had done and why, and that he was grateful to her for listening to Rodney's explanation of why her plan wouldn't work. He stressed that she had saved his life. When he began to sense a shift in emotion, he assured her that he would stay around for as long as possible. Although he warned her that he couldn't promise her he'd keep safe, he did vow to do his best to come back to her each and every time. Just as the connection began to slide back toward the familiar, Rodney interrupted.

"Colonel, answer me! Are you all right or not?"

John smiled and cracked his eyes open. "Fine. I just had to clear up a bit of confusion before we started. And she says hi."

Rodney's expression immediately softened. "Oh, well, okay. She really said hi? Tell her hi back from me. And then we're ready to start making the changes to the power grid."

John nodded and closed his eyes again. "I'm ready. Just tell me what you want."

oOo

"Colonel, it's been two hours. You need to quit."

John recognized Dolon's voice, but didn't open his eyes. "Hang on just a few more seconds. Almost done."

Rodney wondered if he should make Sheppard stop or let him finish when his radio activated.

"_Rodney, it's Elizabeth. Earth is dialing in."_

"On our way. Thanks, Elizabeth." Rodney stood and walked over to the weapon's chair. "Okay Sheppard, the new people are arriving, so we need to go."

John opened his eyes and sat up. "We're done. You might want to double check, but I think it's good." John stood, keeping one hand on the arm to counter the expected head rush. It passed quickly and he grinned at the frowning scientist. "Come on, Rodney, we have people to greet."

"We'll check the modifications while you get the new people from Earth settled," said Dolon.

"Good," responded Rodney as they headed for the door. "I'll be back when we're finished with the meet and greet and you can fill me in on whether it worked or not."

Dolon and Radek watched the two figures disappear out the door. "Yes, Master," said Radek, bowing toward the door. Dolon nearly fell out of his chair laughing, earning a grin from Radek, who didn't remember ever seeing the man show so much emotion.

"I think we corrupt you," said the Czech scientist, before joining the Ancient with his own laughter.

oOo

John and Rodney arrived at the gateroom as the wormhole shut down. They stood to one side as Helia and Elizabeth greeted the newcomers, before calling for the two to take over. John noticed Savill, Ronon, and Teyla joining them as they walked out to the ten new people and their luggage.

"Hey guys, just in time." John gave them a nod and noticed them fall in behind him and Rodney. The ten people from Earth turned to face the group as they came to a stop and spread out in a line. Five scientists stood beside five military personnel. All had been previously stationed on Atlantis, as Helia still did not want new, untried people in the city, a point both John and Rodney understood and agreed with. They had discussed letting untested people come at a later time, when things were more settled and established.

"I'm sure you all remember, but I'm Lt. Colonel John Sheppard and this is, of course, Rodney McKay. Those of you who are scientists will be under Dr. McKay and military personnel will under my command. The two of us are still under Dr. Weir, as before, but the city is under complete control of the Ancients. Captain Helia, who you met just a moment ago, is the final authority in the city. Military will also be working with Teyla Emmagan and Ronon Dex, as you did before. This is Savill and he's second in command of Atlantis. If he tells you something, you'd better listen. He has final military say in the city, except of course for Captain Helia. Basically, your chain of command is to go to either Dr. McKay or myself, followed by Dr. Weir, and then Captain Helia. Is that clear?"

There was murmurs of agreement and a lot of head nodding. "Good. Just remember that we are here at the discretion of the Ancients and they can send us packing any time they like, so behave appropriately. You might find yourself having slightly less freedom than before, but they have gone out of their way to make us welcome, so play nice. We'll have a formal orientation session tomorrow morning at 0800 in the main conference room. Be there. You can check in at the conference room for your assignment to quarters and let one of us know if you have any questions. Dismissed."

The group once again began talking amongst themselves as they moved toward the stairs. "What if I'd wanted to say something? You didn't even give me a chance."

John glanced at Rodney. "_Do _you want to say anything to them?"

Rodney shrugged his shoulders. "Well, no, but that's beside the point. You should have at least offered."

John sighed and saw Ronon laughing as he stood behind Rodney. "I'm sorry, Rodney. I'll be sure and offer you a chance to speak next time."

Rodney nodded, seemingly placated for the moment. John turned to face Major Lorne, who had come up to stand beside him. "Welcome back, Major. Did you miss us?"

Lorne looked around the gateroom and control room above and smiled. "Actually, I did miss this place. It's good to be home, sir."

John grinned and slapped him on the shoulder. "I know exactly what you mean. Do you have something for me?"

Lorne nodded and handed John a rather flat box that looked almost like a medium pizza box. "Yes, sir, right here. General Landry said he checked it himself and the part he could read looked okay."

John took the box and gave a small nod. "Thanks. You'd better see to your quarters and I'll see you in the morning, unless you want to meet us for dinner in the mess hall later."

"Actually, I'd like that sir. I'm anxious to hear what you've been doing all these weeks. There's a rumor going around Earth that you got some important medal from the Ancients."

"It is true," said Teyla. "And it is quite beautiful. You should have the Colonel show it to you."

John blushed. "No one wants to see that."

"What, the medal? Then it's true?" Lt. Carmichael stopped beside Lorne, grinning widely and prompting Lorne to bite his lip to keep from laughing. "Wow, that's really cool, Colonel. Could we see it later?"

John shifted his weight from one foot to the other. "Sure, later," he mumbled.

"Great, I'll tell the guys," the Lt. said as he hurried off to join the others.

John just sighed. "Kids."

Ronon clapped John on the back, knocking him off balance so that he had to take a couple of steps forward to keep from falling while clutching the box in his hands. "That's what you get for playing hero."

John regained his balance and turned back to face the others. "Could we just go do this?"

Elizabeth had walked up to join them and smiled at John. "Carson is on his way."

"I'm off to get my room. I'll try to catch you later," said Lorne as he headed up the stairs. A few seconds later, Carson hurried out to join them.

"All right, I'm here. Are we going now?"

John looked at Elizabeth and then they both nodded. "Might as well," he said. John and Elizabeth began walking up the stairs, followed by Rodney and Carson, and then Teyla and Ronon. When they reached the top, John knocked on the doorframe to Helia's office. Helia noticed the crowd around the door and stood, motioning them in.

"Colonel, Dr. Weir, what can I do for you?"

John and Elizabeth moved to stand in front of Helia's desk with the others fanning out around them. John looked at Elizabeth, who gave him a nod to begin. He cleared his throat as he turned back to the Ancient captain. "Captain Helia, we were very honored a few weeks ago when you granted us citizenship to the city of Atlantis. You took us in when you didn't have to and you let us stay. Although we didn't really trust each other at first, all of that has changed and I think we've built a good working relationship." John looked down at Elizabeth, giving her a brief nod.

Elizabeth continued. "You publicly declared your trust in us when you granted us citizenship with all its rights. We wanted a way to publicly declare our trust in you and we also wanted to thank you for everything you've done for us. We weren't sure how you'd feel about this, but on Earth it's customary to give others a plaque when honoring them. People usually display them by hanging them on a wall."

She turned to Rodney, who'd taken over the box when they'd reached the top of the stairs. He opened the box and pulled out a wooden plaque with a picture at the top and writing on a metal plate beneath. Handing it to Elizabeth, she took it around and stood beside Helia, holding the plaque so all of them could see. At the top was a picture of the six of them, with John in the weapon's chair and the others standing around it.

"Radek took the picture for us," said Rodney. "We thought the chair room was an appropriate place, since it's been kind of important since we got here."

Beneath the picture was writing in Ancient, and then an English translation below that. Elizabeth cleared her throat. "We weren't sure if should get it in English or Ancient, so we did both. It says _We pledge our loyalty to the city of Atlantis and her inhabitants and we will always do our best to protect her. Thank you for letting us call Atlantis home._" Each of their names appeared below the English version of the text.

Elizabeth handed Helia the plaque and she stood staring at it for a long time. John began to get nervous, fearing that they had somehow offended her. He could tell from the furtive glances of the others, they were also getting worried. Helia ran one finger along the engraved surface, studying it. She finally raised her eyes and looked at them.

"Thank you. I did not expect you to do anything, but I appreciate this honor. The fact that you feel so strongly makes me even more committed to my decision to make you part of Atlantis. I have to admit, I find myself more and more excited about the possibilities for the city." She looked back down at the plaque. "You say I should hang this on the wall?"

John nodded, relief filling him. "Yeah. I can help you with that, if you like."

Helia smiled and nodded. "Yes, I would like that very much. Thank you, all of you, for this gift. I believe I would like to hang it in the control room instead of my office, however, so more people may see it."

Elizabeth let out a deep breath and grinned. "Yes, that would be fine. I'm glad you like it. We weren't sure of the best way to show our appreciation, but we wanted to do something."

"You have done well."

John clapped his hands together. "Well, I'll go get a couple of things and then you can show me where you want to hang it. Be back in a jiffy." They all filed out of the office, grinning and nodding to one another at the success of their little project. Helia watched them go.

A few moments later, Savill stepped in and walked over to her desk, looking down at the plaque. He read it and grinned.

"You knew about this?" asked Helia.

Savill shrugged his shoulders. "Sort of. I knew they were up to something, I just wasn't sure what. That's really nice."

Helia looked at it and nodded. "Yes, it is. I must admit, they caught me off guard. These humans are full of surprises."

Savill watched her for a moment, a tiny smile turning up the corner of his mouth. "So, what do you think?"

Helia gave a small snort. "I think we made a very wise decision letting them stay and I think, with their help, Atlantis may actually be restored to a lot of her former glory. They have proven to be much greater allies and help than I would have imagined." Helia smiled and nodded her head. "The future doesn't look quite so bleak as I first feared."

oOo

John stepped through the gate and into the gateroom of Atlantis. He immediately felt a rush of emotion that left him a little light headed. Staggering a step before getting his legs working again, he grinned. _Yes, I'm home and I'm safe._ He almost felt Atlantis giggle.

"John, are you all right?"

Taking a deep breath, he looked up to see Elizabeth walking toward him. "Fine, just a . . . interesting welcome home. She gets a little more nervous when I go off world these days." He'd been back on full duty for several weeks now with no mishaps, but Atlantis apparently "worried" about him when he was off world. He'd begun to realize that he'd felt the worry and the relieved welcome back before the return of the Ancients, but it had been much more subtle and easy to ignore. His return to the city to fight the Asurans had awakened a much deeper connection that he was still exploring and getting used to.

"Oh, brother," muttered Rodney from behind him. "He even has Ancient cities swooning over him."

John spun around, a frown on his face. "It's not like that, Rodney, and you know it."

Rodney rolled his eyes and tilted his head. "Yeah, okay, so it's not really like that. But my version is certainly more interesting."

John stared at Rodney for a few seconds before letting his head drop forward. "I have no idea why I keep trying."

Ronon snickered, but Teyla stepped forward to take John by the arm. "Rodney is an acquired taste and we have merely been exposed to him enough to accept him."

Rodney grinned and nodded once before stopping and sobering. "Wait, what do you mean by that?"

"She just means that we all have our peculiarities and we've been together long enough to accept each other the way we are," said Elizabeth, tapping into her diplomatic experience.

"Yes, that is what I mean," agreed Teyla.

"Oh, okay. I guess."

John felt one side of his mouth twitch upward in a crooked grin. "She's right, you know. When you think about it, we're kind of an odd group."

Ronon snorted loudly. "You people, maybe. I'm perfectly normal."

They looked at him silently for about three seconds before bursting out in laughter that drew the attention of the Ancients in the control room. About the time they calmed down, they looked up to see Helia coming down the steps. "Dr. Weir, Colonel Sheppard, may I see you and the others?" She immediately turned and went quickly back up the steps.

John looked at Elizabeth. "What's going on?"

Elizabeth shrugged her shoulders. "I have no idea, but I think we'd better go find out."

They entered the conference room a minute later to find Helia talking to Savill and a technician, Dolon working on a computer at the far end of the table. As they spread out to take seats, the technician left and Helia turned to them. "We have a problem."

Elizabeth glanced at John and then back to Helia. "What is it? Can we help?"

Helia nodded. "I'm counting on it. We brought up some of our long range sensors we have planted around the galaxy and we've received information indicating the Asurans are planning another attack. They are still constructing their attack ships. We cannot allow them to reach Atlantis again, so I plan on taking the _Tria_ to launch an attack on them."

John sat up ramrod straight, confusion on his face. "Wait a minute, the _Tria_? I thought that was destroyed in the last fight with the Replicators."

Helia shook her head. "No, the _Tria _was in dry dock for repairs when they attacked. We have since repaired her and added some modifications, thanks to the help of Dr. McKay. He and Dolon have modified the weapon systems so that they can send out a pulse we hope will work similar to the weapons you brought from Earth."

John's mind was whirring so fast it almost made him dizzy. "Wait a minute. You worked on the _Tria _and didn't say anything? When was this?"

Rodney sighed and looked as if he was trying to be patient. "Hello, five weeks in a stasis pod. What did you think I did all that time, sat and held your hand? Sorry, but no. I was helping develop and install a weapon system to fight the Asurans. We had to alter the pulse frequency from what we used when we took back Atlantis and change the delivery system enough they wouldn't anticipate it. And it's quite ingenious, if I do say so myself." Rodney crossed his arms and grinned proudly.

John rubbed the side of his head. "You'd think someone would have mentioned that to me by now. I can't believe you missed the opportunity to brag."

Rodney grunted. "Too much time had passed by the time you were coherent. I had moved on to other projects and forgot you didn't know."

John turned back to Helia. "That still seems awfully risky. Are you sure you want to go after them on their home turf?"

"They can't be allowed to reach Atlantis again," said Savill. "They almost destroyed the city the last time." His eyes were dark, his jaw clenched in anger.

"What about Atlantis?" asked Elizabeth.

Helia let out a deep breath. "That is why I need you. Savill and I will take most of our people on the _Tria._ We will only leave a small group of scientists that we do not need and are presently engaged in important research here. I am asking that you take over Atlantis in our absence. I have talked with you both and you have allowed me to read many of your reports. I believe the structure you had in place before worked well, so I would like for that to be reestablished. Dr. Weir, you will be in charge of the city with all military matters going to Colonel Sheppard. I get the impression that you made many joint decisions and sometimes worked as a group to determine the best course of action and I think that a wise arrangement. I will make it clear to your government that Atlantis remains ours and that you are the only ones I will accept as caretakers."

"I am also aware that, even with the personnel added recently, you will need more to effectively run and protect the city, so I am authorizing you to bring in additional people. I will leave the numbers and choices to you, but everyone must be approved by you. I'm sure Dr. McKay can help select scientists and Dr. Beckett the medical personnel. I need it to be clear to your government that if we return and they have usurped your authority and sent in others of their choosing to run our city, all connections and negotiations with Earth will be immediately and permanently terminated. I will not tolerate any variation in my conditions."

They sat in silence for a moment, letting the news sink in. Elizabeth finally snapped out of her haze. "Of course, we'll be happy to help. Is there anything else we can do?"

Helia smiled and shook her head. "I do not believe so. The knowledge that you will care for our city and protect it, if the need arises, is help enough. I am hopeful that your assistance with the new weapons will allow us to have a final victory over the Asurans. Now, with your agreement, I will need to contact General Landry so he can get the information to your President. If they agree, and I believe that they will, we will need to meet again to make the final arrangements." With a small nod, she hurried out of the room, Savill right behind her.

John sat staring into space for a few moments. "Wow. I didn't see that one coming."

oOo

John, Rodney, Teyla, and Ronon took one last look at the _Tria _before leaving the large docking station and entering the hallway. It had been four days since Helia had called them in to announce she was leaving Atlantis in their care so the Ancients could go after the Asurans. John had been amazed at the preparations that had taken place in the relatively short space of time.

"It's going to be weird around here," said Rodney.

John nodded. "Yeah, I know what you mean. I've gotten pretty used to the Ancients being here. I guess you'll miss Dolon. You two seem to have really hit it off."

"McKay argues with and insults Dolon almost as much as much as he does with you, Sheppard," remarked Ronon.

Rodney scowled at Ronon before turning back to John. "He's okay. At least he's relatively intelligent, a quality sadly lacking in most of my staff. He usually manages to know what he's talking about. I guess the warrior set will miss Savill. I've seen you four hanging around like some kind of gang, usually sweaty and dirty and disgusting."

"Savill is remarkable soldier," said Teyla. "I will miss sparring with him."

John smirked and nudged Ronon in the ribs lightly with his elbow. "Yeah, I bet you will. And the after workout dinners as well."

"Rodney's eyes widened and he turned to the blushing woman. "You had after workout dinners with Savill? Why didn't anyone tell me?"

"There was nothing to tell," said Teyla firmly, creasing her brow into a dark frown. "Savill and I merely shared a meal or two."

Ronon chuckled. "Yeah, just a meal." He returned the nudge to Sheppard's ribs, but did so forcefully enough to make John stagger. John quickly got his balance back and shot a dark look at Ronon, who completely ignored him.

The lights flickered a little, then blazed brightly. Rodney snorted and looked back to John. "I thought you said you talked to her."

John shrugged his shoulders. "I did. She knows we aren't abandoning her again, but all this loading-up-to-leave activity makes her nervous."

"I don't remember Atlantis being this sensitive before the Ancients came," said Ronon. "It seems like she reacts to things more than she used to."

"Hello. Three charged ZedPMs versus one partially charged one. She was barely awake enough to function," said Rodney.

"And I'm sure the Ancients initiated some functions that we didn't even know were there," added John.

Rodney waved one hand dismissively. "I'd have figured it out. The main problem was the power, or rather the lack of power."

They reached the corridor with their quarters and stopped, forming a circle in the middle of the hall. "Okay, let's get cleaned up and then we'll go to dinner. I think Elizabeth is meeting us there about 1800," said John.

"What about Dr. Beckett?" asked Teyla.

Rodney snickered and looked at John. "I think he has other plans."

oOo

Carson finished stacking bandages on the shelf and then looked down into the empty box on the floor. "That's the last of it. Your infirmary is now fully stocked with supplies."

Emira finished entering information on her data pad. "All right, we're also fully inventoried. Carson, I can't thank you enough for your help. I could never have gotten this place ready this quickly without you."

Carson walked up to stand in front of her. "Nonsense, you'd have done fine. But I was happy to help. Now, since we've barely slept in four days, I think it's time for a break. How about dinner?"

Emira set the data pad down on the table and looked directly at Carson, smiling. "Sounds good."

Carson locked eyes with her, never moving his gaze as he slipped his left hand through her hair and behind her head, gently pulling her forward as he leaned over and kissed her. As soon their lips touched, she leaned forward against him, pushing her body and her lips against his. She placed her arms around his neck as he put his other hand against the small of her back, pressing her body up against his and eliciting a small moan from her.

The sound of a throat clearing interrupted their moment. Carson pressed her even more tightly against him for a second before releasing her. They separated like an opening book, his right arm not leaving its place at her waist while his left side backed away until he could see an uncomfortable Helia and Elizabeth standing in the doorway.

"Hello Elizabeth, Captain Helia," he said calmly, trying his best to act like this was perfectly normal.

Helia finally looked up to make eye contact. "Emira, I just wanted to see how things were going here."

Emira coughed and cleared her throat, trembling slightly against Carson's grip. "Good. We just finished stocking and inventorying. The infirmary is ready to go, ma'am."

Helia gave a short nod. "Good work. Everything seems to be on schedule, so we'll depart at 0800 tomorrow as planned."

"Yes, ma'am. I'll be ready."

"Final debriefing for all section leaders will be at 1930 hours."

Emira nodded. "I will be there."

Helia smiled and twitched one eye slightly. "Carry on."

Carson thought he saw Elizabeth stifling a laugh as she followed Helia out the door. The two doctors stood stiffly for several moments until they were sure the two leaders were well down the hall. As they relaxed, breathing out a long sigh, Emira began to giggle.

"Emira, that was not funny. That was bloody embarrassing," Carson said sharply. He watched Emira try to straighten her face and be more serious, only to start laughing again. Tears streamed down her face and she finally just sat in the floor, doubled over. After a few moments, Carson joined her, the giggles hitting first as he remembered the look on Elizabeth and Helia's face. They had been even more uncomfortable than the two doctors they caught kissing. And then he thought of the absurdity of two consenting adults being embarrassed about kissing. Pretty soon, Carson was sitting on the floor beside Emira. Every time one of them began to sober up, the other would get them laughing again.

One of the ship techs stepped into the infirmary and stopped dead in his tracks at the sight of the two doctors having a giggling fit in the floor. He paused with his mouth open a second and then lifted one finger. "I can come back."

As he left, silence filled the room. Emira and Carson looked at the empty doorway for a second before looking at each other. "I think we scared him," said Emira.

Carson looked at her a few seconds and then they both began to laugh again.

oOo

"I'll take good care of her for you," said John.

"I know you will." Savill looked longingly at the city he was leaving behind.

"I wish we'd gotten a chance to train more together. You guys have some pretty cool moves."

Savill gave a small nod. "As do I. I was also looking forward to traveling through the gate on more missions together. Your methods are somewhat unconventional, and yet they often seem to work."

"Yeah, well, when you get back." John swallowed hard, knowing full well he might never see Savill or anyone else on the _Tria _again. They all had high hopes for success, but the Pegasus Galaxy had a way of knocking you on your butt when you least expected it. He scanned the faces before him, trying to memorize every one. Many of the crew had already boarded the large ship on the hanger deck, but several still stood outside, saying their goodbyes. The Ancients and humans had formed a strong bond in the short time they had lived and worked together.

As Savill talked to Ronon and Teyla, John glanced around to see Dolon saying his farewells to Rodney and Radek, all three men looking decidedly sad. He smiled when he noticed Emira and Carson kissing, locked in a tight embrace at the edge of the crowd. He wanted to drift over and kid them with a worn out phrase like "Get a room," but he couldn't bear to ruin what might be their last moment together. He took a deep breath, telling himself not to think like that. John had seen too much death and despair in his lifetime and it was hard not to lean that way.

"Don't worry, we will be back before you've had time to miss us," Savill said to Teyla. "And then you must show me more of your stick fighting." It was hard to miss the emotion in his eyes as he tried to look stiff and formal.

"I will look forward to it," she said, her voice quivering just a little. She leaned forward and Savill followed, their foreheads touching for several seconds. When they leaned back, Teyla looked up at the man. "Be safe."

Savill smiled. "I will." He looked up at Ronon and John. "And I expect the three of you to watch each other's back and be here when I return."

Ronon nodded. "It's what we do." He held his hand out and they grabbed each other by the forearm in friendship. After a few seconds, Savill moved down to John to repeat the maneuver. When they released their grip, John saluted Savill and waited until the action was returned.

"I have to go now," Savill said roughly, turning to walk quickly up the ramp to the ship, never slowing or looking back.

John stood with his friends, feeling a little lost. He saw Helia and Elizabeth coming toward them and took a few steps to meet them. "I guess you're almost ready."

Helia nodded as they came to a stop. "Yes, we are. I'm just about to board and give the final call for everyone else to make ready. I just wanted to thank you again for taking charge of the city. We'll contact you as soon as we know anything. We have relay stations along the way and we'll be able to get messages through to let you know if it seems the Asurans might get past us."

John grimaced, rolling his upper lip in for a second. "We'll be ready for them. If they get this far, they'll wish they hadn't. Rodney's got some ideas on ways to fortify the defenses."

"That's why I will not worry about Atlantis. I know she is in good hands." Helia gave a short bow. "And now, it is time."

"Break a leg," said Elizabeth.

Helia frowned and tilted her head. "You want me to break my leg?"

Elizabeth flushed and stuttered as she tried to explain. "No! No, of course not. It's an old saying, from the theatre. It means . . . oh, never mind. Just . . . keep safe and come back."

Helia shook her head in confusion and then smiled. "We will do our best." She turned and motioned to some of the others who were watching before heading up the ramp. As some of the Ancients began walking up the ramp, the other Ancients took notice and slowly began to join them.

"Break a leg?" John asked with a grimace.

Elizabeth shrugged her shoulders, he face flushing warm with embarrassment. "I know, it goes along with my bedside manner."

John nodded, watching Dolon make his way into the ship. He saw Carson walk Emira to the end of the ramp. She was the last one to break away and enter the _Tria, _the door closing moments after she boarded. The humans and the handful of Ancients remaining behind made their way off the dock and into the hallway, lining up at the windows to watch the departure. Several minutes later, the floor rumbled with the start of the engines and they watched the ship shudder and slowly make its way out of the open canopy above. Once it cleared Atlantis and gained some altitude, there was bright flash and it was gone.

John watched in silence, Elizabeth and Teyla on one side of him, Rodney and Ronon on the other. They stood looking at the sky until the overhead canopy closed. People around them began talking again, wandering off in small groups. Carson came up to join them, his expression pained.

"You gonna be okay, Doc?" John asked.

Carson sighed. "Aye, I'll be fine. I'll really miss her though."

Rodney studied Carson for a moment. "You two spent a lot of time together the last few days. So, did you ever . . . you know?"

"Rodney!" chorused John and Elizabeth. John frowned and shook his head.

Carson stared at Rodney silently for several seconds and then smiled, smacking Rodney firmly on the back. "Son, that is something you will _never_ know." Then he walked down the corridor.

"Rodney, it was not your place to ask such a question," scolded Teyla.

"What? I was just interested . . . you know, as a friend," Rodney defended.

Elizabeth shook her head and pressed her thumb and finger against the bridge of her nose. "Oh, Rodney," she mumbled.

John turned and looked out the window at the empty place that had been occupied by the _Tria _and a hundred people just minutes before. It fit with the empty spot that seemed to exist in Atlantis now. "Let's go," he said, not wanting to dwell on the people that were gone or the likelihood of their return. He began walking down the hall and felt comfort in the sound of the footsteps behind him.

oOo

John felt the connection slide into place. It was the middle of the night, but he hadn't been able to sleep. After talking with his team until almost midnight, he'd been too wound up to drift off. He felt a similar sense of unease with Atlantis, bringing him to the chair room for a little meeting. The city was unsettled, with flickering lights and sputtering control panels. John reached out to Atlantis, seeking to comfort her as much as to be comforted. He smiled as they eased each other's tension, remembering how they had been able to keep Atlantis going with only one ZPM and a whisper of the connection they possessed now. This should be a cake walk, John reasoned.

An hour later, John returned to his room. The lights were no longer flickering and they were both more relaxed. He knew they could make it work, with or without the Ancients. And he felt a renewed sense of confidence in the mission of the _Tria_, thinking in terms of when they returned instead of if. He climbed into bed, exhausted, but feeling like maybe everything would be okay. As he snuggled himself into a comfortable position, he found himself smiling.

Tomorrow would be a busy day. They had to wade through a bunch of folders choosing which personnel to ask back to Atlantis. New schedules had to be arranged to cover all vital posts until the new people arrived. Quarters would have to be arranged. Rodney had to reassign research priorities. Missions had to be prioritized and set up. They needed to reexamine the food situation and see if they needed to start runs from the _Daedalus_ again. Yeah, a very busy day and on almost no sleep. Feeling the touch of the city, John couldn't help but think about how much he loved his job.

THE END


End file.
